Solver behaviour when giving fixed variable a start value

Dear Gurobi staffers,
my model is a capacity expansion of a power plant to meet a given electrical demand for an entire year (8760 timesteps). In general I model existing components (only variable costs) and new component options (also investment costs). Lets say I have two options. Option 1 already exists option 2 is an investment option.
For each option I use an integer variable to modell its existence. Integer because for each option multiple blocks might be modelled. (code examples in Pseudo-Julia/JuMP-code)

# Variable declaration:
@variable(model, I_1>=0,Int)
@variable(model, I_2>=0,Int)

Lets say option 1 consists of 2 blocks and option 2 should be less than 10 blocks it gives. Due to easier programming I add these as constraints, rather than fixing the variable upon declaration( but from my point of view it shouldn't make any difference)

@constraint(model, I_1 == 2)
@constraint(model, I_2 <= 10)

To aid the solver and assuming that it is cheaper to first use the already existing components rather than new ones, I provide start values for existence Variables:

set_start_value(I_1, 2)
set_start_value(I_2, 0)

which then Gurobi uses to process the MIP start and improved model performance significantly. The start_value for I_1 was actually never really intended, but as my actual model is more complicated and uses variable-sets and arrays, it was easier to simple set start values for all existence variables then rather the new ones.

So far so good and everything works as expected. Now comes what I did not expect:
When I run my model for past years, I do not give the model any investment options, because all capacities are known and fixed. However, as i use the same code structure, the start_values are set anyway, however all variables are already fixed to the same start value using the equality constraints anyway. The code would now look like this:

# Variable declaration:
@variable(model, I_1>=0,Int)
@variable(model, I_2>=0,Int)

@constraint(model, I_1 == 2)
@constraint(model, I_2 == 3)

set_start_value(I_1, 2)
set_start_value(I_2, 3)

I had assumend that providing start_values for fixed variables would not influence the solver behavior, but it does. I ran the model two times it completely identical settings (same computer, solver settings and model). The only difference is that in the first run I used the option set_start_values and I did not use start_values in the second run.

Here is the log file of the run when providing the start values:

Gurobi Optimizer version 9.5.0 build v9.5.0rc5 (linux64)
 Thread count: 16 physical cores, 32 logical processors, using up to 2 threads
 Optimize a model with 3661558 rows, 1927245 columns and 14409595 nonzeros
 Model fingerprint: 0x6292d718
 Variable types: 1454192 continuous, 473053 integer (78844 binary)
 Coefficient statistics:
   Matrix range     (1e-04, 3e+03)
   Objective range  (1e+00, 1e+00)
   Bounds range     (0e+00, 0e+00)
   RHS range        (1e+00, 5e+06)
 
 Warning: Completing partial solution with 473040 unfixed non-continuous variables out of 473053
 Processing user MIP start: 0 nodes explored in subMIP, total elapsed time 5s

 [removed a lot of MIP start lines to shorten the log] 

 Loaded user MIP start with objective 1.24075e+06
 Processed MIP start in 1409.45 seconds (1068.25 work units)
 
 Presolve removed 1200169 rows and 1252725 columns (presolve time = 5s) ...
 Presolve removed 2542053 rows and 1339089 columns (presolve time = 10s) ...
 Presolve removed 2867602 rows and 1349287 columns (presolve time = 15s) ...
 Presolve removed 2867602 rows and 1350494 columns (presolve time = 21s) ...
 Presolve removed 2867602 rows and 1350494 columns (presolve time = 25s) ...
 Presolve removed 2867602 rows and 1350494 columns
 Presolve time: 29.67s
 Presolved: 793956 rows, 576751 columns, 2632070 nonzeros
 Variable types: 340231 continuous, 236520 integer (131400 binary)
 
 Concurrent LP optimizer: dual simplex and barrier
 Showing barrier log only...
 
 Root relaxation presolved: 793956 rows, 576751 columns, 2632070 nonzeros
 
 Root barrier log...
 
 Ordering time: 0.39s
 
 Barrier statistics:
  AA' NZ     : 5.305e+06
  Factor NZ  : 1.527e+07 (roughly 700 MB of memory)
  Factor Ops : 6.143e+08 (less than 1 second per iteration)
  Threads    : 1
 
                   Objective                Residual
 Iter       Primal          Dual         Primal    Dual     Compl     Time
    0  -7.62927743e+06 -1.71132632e+08  1.08e+03 1.19e+00  1.32e+03  1447s
    1   1.97672504e+06 -1.50404396e+08  2.39e+02 1.24e+00  3.07e+02  1448s
    2   3.48213917e+06 -5.32976621e+07  3.16e+01 3.36e-03  5.14e+01  1448s
    3   3.26102700e+06 -1.06538645e+07  1.48e+00 8.39e-14  8.40e+00  1449s
    4   2.33909588e+06 -5.10697324e+05  1.79e-01 3.91e-14  1.65e+00  1451s
    5   1.72297028e+06  4.20769277e+05  5.25e-02 1.60e-14  7.49e-01  1451s
    6   1.44942959e+06  8.32190087e+05  1.85e-02 7.11e-15  3.55e-01  1452s
    7   1.33821976e+06  9.95055332e+05  8.33e-03 5.33e-15  1.97e-01  1453s
    8   1.28877113e+06  1.08774622e+06  4.30e-03 3.55e-15  1.15e-01  1454s
    9   1.26934444e+06  1.14650793e+06  2.86e-03 5.33e-15  7.05e-02  1454s
   10   1.24263065e+06  1.17876179e+06  1.07e-03 3.55e-15  3.66e-02  1455s
   11   1.23031259e+06  1.19952299e+06  3.87e-04 3.55e-15  1.77e-02  1456s
   12   1.22576674e+06  1.20907925e+06  1.80e-04 3.55e-15  9.57e-03  1457s
   13   1.22402199e+06  1.21321522e+06  1.11e-04 5.33e-15  6.20e-03  1458s
   14   1.22282193e+06  1.21658397e+06  6.76e-05 5.33e-15  3.58e-03  1459s
   15   1.22157807e+06  1.21813298e+06  2.51e-05 5.33e-15  1.98e-03  1460s
   16   1.22116919e+06  1.21942861e+06  1.27e-05 5.33e-15  9.98e-04  1460s
   17   1.22093580e+06  1.21992414e+06  6.20e-06 3.55e-15  5.80e-04  1461s
   18   1.22080466e+06  1.22024207e+06  2.74e-06 5.33e-15  3.23e-04  1462s
   19   1.22072742e+06  1.22043680e+06  9.12e-07 5.33e-15  1.67e-04  1463s
   20   1.22070579e+06  1.22057487e+06  4.16e-07 5.33e-15  7.50e-05  1465s
   21   1.22069845e+06  1.22061181e+06  2.69e-07 3.55e-15  4.97e-05  1465s
 
 Barrier performed 21 iterations in 1465.67 seconds (1101.81 work units)
 Barrier solve interrupted - model solved by another algorithm
 
 
 Solved with dual simplex
 
 Root relaxation: objective 1.220683e+06, 264354 iterations, 25.67 seconds (24.75 work units)
 Total elapsed time = 1470.00s
 Total elapsed time = 1475.04s
 Total elapsed time = 1483.40s
 Total elapsed time = 1487.92s
 
     Nodes    |    Current Node    |     Objective Bounds      |     Work
  Expl Unexpl |  Obj  Depth IntInf | Incumbent    BestBd   Gap | It/Node Time
 
      0     0 1220682.80    0 16968 1240754.01 1220682.80  1.62%     - 1503s
      0     0 1230485.18    0 21429 1240754.01 1230485.18  0.83%     - 1636s
      0     0 1232863.09    0 18121 1240754.01 1232863.09  0.64%     - 1710s
      0     0 1233432.82    0 17866 1240754.01 1233432.82  0.59%     - 1736s
      0     0 1233437.88    0 17906 1240754.01 1233437.88  0.59%     - 1741s
      0     0 1233437.94    0 17912 1240754.01 1233437.94  0.59%     - 1742s
      0     0 1236167.59    0 20597 1240754.01 1236167.59  0.37%     - 1912s
 H    0     0                    1240748.3080 1236167.59  0.37%     - 1917s
      0     0 1237007.40    0 18870 1240748.31 1237007.40  0.30%     - 1944s
      0     0 1237370.64    0 19264 1240748.31 1237370.64  0.27%     - 1969s
      0     0 1237392.93    0 19454 1240748.31 1237392.93  0.27%     - 1972s
      0     0 1237394.83    0 19451 1240748.31 1237394.83  0.27%     - 1974s
      0     0 1239125.19    0 16676 1240748.31 1239125.19  0.13%     - 2125s
      0     0 1239464.95    0 14258 1240748.31 1239464.95  0.10%     - 2140s
      0     0 1239555.02    0 14003 1240748.31 1239555.02  0.10%     - 2146s
      0     0 1239562.00    0 14038 1240748.31 1239562.00  0.10%     - 2148s
      0     0 1239563.15    0 14061 1240748.31 1239563.15  0.10%     - 2150s
      0     0 1240160.50    0 10324 1240748.31 1240160.50  0.05%     - 2212s
      0     0 1240262.90    0 8547 1240748.31 1240262.90  0.04%     - 2222s
      0     0 1240273.09    0 8715 1240748.31 1240273.09  0.04%     - 2227s
      0     0 1240274.91    0 8562 1240748.31 1240274.91  0.04%     - 2231s
      0     0 1240422.86    0 5423 1240748.31 1240422.86  0.03%     - 2284s
      0     0 1240441.66    0 4949 1240748.31 1240441.66  0.02%     - 2293s
      0     0 1240443.64    0 5123 1240748.31 1240443.64  0.02%     - 2298s
      0     0 1240476.38    0 3340 1240748.31 1240476.38  0.02%     - 2338s
      0     0 1240480.23    0 3283 1240748.31 1240480.23  0.02%     - 2349s
      0     0 1240491.32    0 3186 1240748.31 1240491.32  0.02%     - 2388s
      0     0 1240493.26    0 2831 1240748.31 1240493.26  0.02%     - 2399s
      0     0 1240497.35    0 2822 1240748.31 1240497.35  0.02%     - 2434s
 H    0     0                    1240744.0081 1240497.35  0.02%     - 2441s
      0     0 1240498.44    0 2692 1240744.01 1240498.44  0.02%     - 2443s
      0     0 1240500.99    0 2482 1240744.01 1240500.99  0.02%     - 2480s
      0     0 1240501.56    0 2270 1240744.01 1240501.56  0.02%     - 2485s
      0     0 1240503.31    0 2287 1240744.01 1240503.31  0.02%     - 2510s
      0     0 1240503.31    0 2287 1240744.01 1240503.31  0.02%     - 2519s
 H    0     0                    1240671.8692 1240503.31  0.01%     - 2536s
 H    0     0                    1240648.5164 1240503.31  0.01%     - 2745s
 H    0     0                    1240641.9222 1240503.31  0.01%     - 2749s
 H    0     0                    1240626.5463 1240503.31  0.01%     - 2753s
 
 Cutting planes:
   Gomory: 315
   Lift-and-project: 22
   MIR: 33328
   StrongCG: 14
   Flow cover: 13793
   Relax-and-lift: 2136
 
 Explored 1 nodes (489966 simplex iterations) in 2753.66 seconds (2264.25 work units)
 Thread count was 2 (of 32 available processors)
 
 Solution count 10: 1.24063e+06 1.24064e+06 1.24067e+06 ... 1.24083e+06
 
 Optimal solution found (tolerance 1.00e-04)
 Best objective 1.240626546281e+06, best bound 1.240503306683e+06, gap 0.0099%
 
 User-callback calls 171405, time in user-callback 0.40 sec

And  here when no start values were provided

 Gurobi Optimizer version 9.5.0 build v9.5.0rc5 (linux64)
 Thread count: 16 physical cores, 32 logical processors, using up to 2 threads
 Optimize a model with 3661558 rows, 1927245 columns and 14409595 nonzeros
 Model fingerprint: 0xc598e863
 Variable types: 1454192 continuous, 473053 integer (78844 binary)
 Coefficient statistics:
   Matrix range     (1e-04, 3e+03)
   Objective range  (1e+00, 1e+00)
   Bounds range     (0e+00, 0e+00)
   RHS range        (1e+00, 5e+06)
 Presolve removed 2461465 rows and 1258501 columns (presolve time = 5s) ...
 Presolve removed 2858842 rows and 1349287 columns (presolve time = 10s) ...
 Presolve removed 2867602 rows and 1350494 columns (presolve time = 15s) ...
 Presolve removed 2867602 rows and 1350494 columns (presolve time = 20s) ...
 Presolve removed 2867602 rows and 1350494 columns
 Presolve time: 22.00s
 Presolved: 793956 rows, 576751 columns, 2632070 nonzeros
 Variable types: 340231 continuous, 236520 integer (131400 binary)
 
 Concurrent LP optimizer: dual simplex and barrier
 Showing barrier log only...
 
 Root relaxation presolved: 793956 rows, 576751 columns, 2632070 nonzeros
 
 Root barrier log...
 
 Ordering time: 0.19s
 
 Barrier statistics:
  AA' NZ     : 5.305e+06
  Factor NZ  : 1.527e+07 (roughly 700 MB of memory)
  Factor Ops : 6.143e+08 (less than 1 second per iteration)
  Threads    : 1
 
                   Objective                Residual
 Iter       Primal          Dual         Primal    Dual     Compl     Time
    0  -7.62927743e+06 -1.71132632e+08  1.08e+03 1.19e+00  1.32e+03    31s
    1   1.97672504e+06 -1.50404396e+08  2.39e+02 1.24e+00  3.07e+02    31s
    2   3.48213917e+06 -5.32976621e+07  3.16e+01 3.36e-03  5.14e+01    32s
    3   3.26102700e+06 -1.06538645e+07  1.48e+00 7.46e-14  8.40e+00    33s
    4   2.33909588e+06 -5.10697324e+05  1.79e-01 3.55e-14  1.65e+00    34s
    5   1.72297028e+06  4.20769277e+05  5.25e-02 1.60e-14  7.49e-01    34s
    6   1.44942959e+06  8.32190087e+05  1.85e-02 8.88e-15  3.55e-01    35s
    7   1.33821976e+06  9.95055332e+05  8.33e-03 5.33e-15  1.97e-01    35s
    8   1.28877113e+06  1.08774622e+06  4.30e-03 5.33e-15  1.15e-01    36s
    9   1.26934444e+06  1.14650793e+06  2.86e-03 5.33e-15  7.05e-02    36s
   10   1.24263065e+06  1.17876179e+06  1.07e-03 5.33e-15  3.66e-02    37s
   11   1.23031259e+06  1.19952299e+06  3.87e-04 3.55e-15  1.77e-02    38s
   12   1.22576674e+06  1.20907925e+06  1.80e-04 3.55e-15  9.57e-03    38s
   13   1.22402199e+06  1.21321522e+06  1.11e-04 3.55e-15  6.20e-03    39s
   14   1.22282193e+06  1.21658397e+06  6.76e-05 3.55e-15  3.58e-03    40s
   15   1.22157807e+06  1.21813298e+06  2.51e-05 3.55e-15  1.98e-03    40s
   16   1.22116919e+06  1.21942861e+06  1.27e-05 5.33e-15  9.98e-04    41s
   17   1.22093580e+06  1.21992414e+06  6.20e-06 3.55e-15  5.80e-04    41s
   18   1.22080466e+06  1.22024207e+06  2.74e-06 5.33e-15  3.23e-04    42s
   19   1.22072742e+06  1.22043680e+06  9.12e-07 5.33e-15  1.67e-04    43s
   20   1.22070579e+06  1.22057487e+06  4.16e-07 3.55e-15  7.50e-05    44s
   21   1.22069845e+06  1.22061181e+06  2.69e-07 3.55e-15  4.97e-05    44s
   22   1.22069109e+06  1.22064121e+06  1.14e-07 3.55e-15  2.86e-05    45s
   23   1.22068613e+06  1.22067423e+06  3.93e-08 7.11e-15  6.82e-06    46s
   24   1.22068333e+06  1.22067905e+06  1.25e-08 5.33e-15  2.45e-06    46s
 
 Barrier performed 24 iterations in 46.41 seconds (37.02 work units)
 Barrier solve interrupted - model solved by another algorithm
 
 
 Solved with dual simplex
 
 Root relaxation: objective 1.220683e+06, 264354 iterations, 19.13 seconds (24.75 work units)
 Total elapsed time = 50.17s
 Total elapsed time = 61.61s
 Total elapsed time = 65.05s
 
     Nodes    |    Current Node    |     Objective Bounds      |     Work
  Expl Unexpl |  Obj  Depth IntInf | Incumbent    BestBd   Gap | It/Node Time
 
      0     0 1220682.80    0 16968          - 1220682.80      -     -   76s
      0     0 1229914.40    0 21448          - 1229914.40      -     -  184s
      0     0 1232886.23    0 18525          - 1232886.23      -     -  245s
      0     0 1233423.05    0 17983          - 1233423.05      -     -  266s
      0     0 1233437.91    0 17928          - 1233437.91      -     -  268s
      0     0 1233437.94    0 17928          - 1233437.94      -     -  269s
      0     0 1236131.66    0 22082          - 1236131.66      -     -  408s
      0     0 1237191.82    0 20493          - 1237191.82      -     -  435s
      0     0 1237377.85    0 19287          - 1237377.85      -     -  445s
      0     0 1237385.94    0 19239          - 1237385.94      -     -  447s
      0     0 1237386.82    0 19442          - 1237386.82      -     -  449s
      0     0 1239073.15    0 17823          - 1239073.15      -     -  582s
      0     0 1239497.17    0 15147          - 1239497.17      -     -  592s
      0     0 1239556.21    0 13772          - 1239556.21      -     -  597s
      0     0 1239561.04    0 13933          - 1239561.04      -     -  599s
      0     0 1239561.73    0 14050          - 1239561.73      -     -  601s
      0     0 1240135.46    0 11342          - 1240135.46      -     -  656s
      0     0 1240247.69    0 8657          - 1240247.69      -     -  664s
      0     0 1240262.73    0 8817          - 1240262.73      -     -  666s
      0     0 1240265.63    0 8876          - 1240265.63      -     -  668s
      0     0 1240419.12    0 5778          - 1240419.12      -     -  720s
      0     0 1240433.73    0 4897          - 1240433.73      -     -  725s
      0     0 1240435.54    0 4937          - 1240435.54      -     -  727s
      0     0 1240469.40    0 3599          - 1240469.40      -     -  767s
      0     0 1240473.60    0 3253          - 1240473.60      -     -  771s
      0     0 1240488.75    0 3005          - 1240488.75      -     -  794s
      0     0 1240490.28    0 3037          - 1240490.28      -     -  800s
      0     0 1240498.71    0 2862          - 1240498.71      -     -  828s
      0     0 1240499.93    0 2789          - 1240499.93      -     -  834s
      0     0 1240503.18    0 2381          - 1240503.18      -     -  853s
      0     0 1240503.59    0 2504          - 1240503.59      -     -  858s
      0     0 1240506.41    0 2492          - 1240506.41      -     -  879s
      0     0 1240506.41    0 2492          - 1240506.41      -     -  896s
      0     2 1240506.41    0 2492          - 1240506.41      -     -  945s
      3     6 1240508.16    2 2484          - 1240507.67      -   272  951s
      9    22 1240511.26    5 2151          - 1240510.52      -   245  958s
     21    68 1240511.72    5 2101          - 1240510.76      -   143  967s
     67   114 1240514.35    3 2255          - 1240511.11      -  72.3  973s
    113   160 1240511.78    4 2269          - 1240511.14      -  60.1  981s
    159   206 1240513.36    6 2185          - 1240511.26      -  54.0  989s
    205   252 1240511.88    7 2110          - 1240511.28      -  52.0  996s
    251   298 1240511.79    7 2071          - 1240511.45      -  48.6 1003s
    297   344 1240513.98    9 2065          - 1240511.75      -  47.7 1009s
    343   385 1240512.57    9 2080          - 1240511.78      -  45.3 1016s
    384   427 1240512.11    7 2116          - 1240511.81      -  43.4 1023s
    426   471 1240512.12    8 2124          - 1240511.83      -  42.1 1030s
    470   512 1240512.46    9 2074          - 1240511.83      -  41.2 1037s
 
 Resetting heuristic parameters to focus on improving solution
 (using Heuristics=0.5 and RINS=10)...
 
    511   536 1240520.35   26 1695          - 1240511.87      -  40.0 1045s
    535   582 1240525.44   29 1774          - 1240511.87      -  39.3 1061s
    581   623 1240535.23   41 1354          - 1240511.87      -  37.5 1076s
    622   668 1240545.34   51 1186          - 1240511.87      -  35.9 1091s
    667   710 1240564.94   64 1115          - 1240511.87      -  34.3 1106s
    709   753 1240587.17   72 1036          - 1240511.87      -  33.1 1122s
    753   754 1240522.06   26 2492          - 1240511.87      -  32.2 1131s
    755   755 1240521.24   29 16968          - 1240511.87      -  32.1 1211s
    756   756 1240519.15   21 21385          - 1240511.87      -  32.1 1274s
    757   757 1240513.24   13 23156          - 1240511.87      -  32.0 1350s
    758   757 1240518.65   23 20949          - 1240511.87      -  32.0 1401s
    759   758 1240519.56   24 17248          - 1240511.87      -  31.9 1429s
    760   759 1240530.51   43 10746          - 1240511.87      -  31.9 1446s
    761   759 1240514.07   12 3546          - 1240511.87      -  31.8 1451s
    763   761 1240590.79   79 2579          - 1240511.87      -  31.8 1456s
    765   762 1240519.98   22 2524          - 1240511.87      -  31.7 1460s
    767   763 1240519.89   21 2393          - 1240511.87      -  31.6 1503s
    768   764 1240516.23   15 2363          - 1240511.87      -  31.6 1505s
    769   765 1240512.23    9 2333          - 1240511.87      -  31.5 1530s
    770   765 1240516.18   11 2196          - 1240514.79      -  31.5 1555s
    772   767 1240519.46   22 2370          - 1240515.02      -  31.4 1562s
    773   767 1240551.71   72 2029          - 1240517.45      -  31.3 1577s
    774   768 1240519.68   19 2017          - 1240517.56      -  31.3 1582s
    775   769 1240524.24   23 1979          - 1240518.30      -  31.3 1598s
    776   769 1240527.16   36 1989          - 1240518.39      -  31.2 1603s
    777   770 1240518.67   22 1985          - 1240518.67      -  31.2 1619s
    778   771 1240544.96   55 2002          - 1240518.69      -  31.1 1624s
    779   771 1240518.92   15 1987          - 1240518.92      -  31.1 1640s
    781   773 1240519.00   20 1952          - 1240519.00      -  31.0 1659s
    782   773 1240519.02   10 1974          - 1240519.02      -  31.0 1664s
    783   774 1240520.93   23 1972          - 1240519.04      -  30.9 1679s
    784   775 1240522.45   26 1972          - 1240519.04      -  30.9 1683s
    785   775 1240519.04   13 1972          - 1240519.04      -  30.9 1690s
 H  785   735                    2736985.0980 1240519.05  54.7%  30.9 1784s
 H  785   698                    1240617.8008 1240519.05  0.01%  30.9 1796s
 
 Cutting planes:
   Gomory: 247
   Lift-and-project: 68
   Projected implied bound: 14
   MIR: 24262
   StrongCG: 6
   Flow cover: 9084
   RLT: 13
   Relax-and-lift: 1794
 
 Explored 785 nodes (899093 simplex iterations) in 1796.53 seconds (2090.51 work units)
 Thread count was 2 (of 32 available processors)
 
 Solution count 2: 1.24062e+06 2.73699e+06 
 
 Optimal solution found (tolerance 1.00e-04)
 Warning: max constraint violation (7.8263e-06) exceeds tolerance
 Warning: max bound violation (6.7371e-06) exceeds tolerance
 Best objective 1.240617800791e+06, best bound 1.240519046854e+06, gap 0.0080%
 
 User-callback calls 206724, time in user-callback 0.27 sec

Providing the start values leads to a faster first solution (after 1500 s instead of 1700 s in the second case), but takes longer to get to the desired MIP-gap. Additionally the run without start values leads to numeric warnings, while the one with start values does not give any warnings.

How can these differences be explained? Is a different solver strategy used to solve the MIPstart before the presolve then after? Is the presolve influenced by the result of the MIPstart? After presolve the model in the first run is as tight as the model in the second.