I've also anecdotally noticed that different cargo
targets can address different subsets of code, a slightly different example: Did feature unification bit me hard?.
The only advice I'd give here, which you may already be doing, is to take the CI aspect out of the loop and test everything locally on windows using a Linux docker. It's so much less painful :-).
I'd also suggest a MRE (Minimal reproducible example - Wikipedia) so people can download and debug locally.
Good luck!