Unfortunately it is not quite that simple. While I need just one feasible solution for each equivalence class of solutions, each set of start values I use could potentially lead to several nonequivalent solutions. I am convinced that the partialmipstart is not a good tool for what I am trying, I had misunderstood how they were used. Fortunately I think I can either make a copy of my model and fix my variables in the copy, or else name these constraints in a way that they are easy to programmatically remove and replace.
(Basically I am working with a large graph, looking for special vertex sets; if I know my special set will contain a k-clique, I can look at all of the k-cliques of the graph and take one representative from each orbit under the automorphism group to use as a start. But I do not know that a k-clique will uniquely determine the set I am looking for.)
I'm confident I am okay working within the tolerances (definitely no weird values in my model), I just wanted to make sure I had the settings correct so that I am not ignoring part of the search tree.
I have attached some of my output; in this example I had not imposed a size restriction so the zero vector was a trivial optimal solution.
Presolve time: 0.01s
Presolved: 41 rows, 81 columns, 1026 nonzeros
Variable types: 0 continuous, 81 integer (81 binary)
Root relaxation: objective 0.000000e+00, 74 iterations, 0.01 seconds
Nodes | Current Node | Objective Bounds | Work
Expl Unexpl | Obj Depth IntInf | Incumbent BestBd Gap | It/Node Time
* 0 0 0 0.0000000 0.00000 0.00% - 0s
Optimal solution found at node 0 - now completing solution pool...
0 0 - 0 0.00000 0.00000 0.00% - 0s
0 0 - 0 0.00000 0.00000 0.00% - 0s
0 2 - 0 0.00000 0.00000 0.00% - 0s
86174 3444 - 33 0.00000 0.00000 0.00% 1.9 5s
143417 5281 - 41 0.00000 0.00000 0.00% 1.8 10s
186948 5974 - 31 0.00000 0.00000 0.00% 1.8 15s
224275 6404 - 38 0.00000 0.00000 0.00% 1.8 20s
256517 6258 cutoff 30 0.00000 0.00000 0.00% 1.8 25s
284810 6892 cutoff 46 0.00000 0.00000 0.00% 1.8 30s
310984 7442 infeasible 35 0.00000 0.00000 0.00% 1.8 35s
335080 7527 infeasible 44 0.00000 0.00000 0.00% 1.7 40s
358430 7791 - 35 0.00000 0.00000 0.00% 1.7 45s
379985 7925 - 35 0.00000 0.00000 0.00% 1.7 50s
401791 8604 - 44 0.00000 0.00000 0.00% 1.7 55s
422596 8650 infeasible 40 0.00000 0.00000 0.00% 1.7 60s