By the way, I don't mind maintaining this patch outside of Gambit, just thought I'd share it here in the case that it's useful.
So my patch, on _any_ mingw system (which might be too broad), changes to ___GAMBITDIR variable to a native windows path, with forward slashes instead of backslashes, while not effecting the --prefix variable at all
I plan to get a build of gambit 4.8.8 with my patch into MSys2 somewhat soon. If my patch is useful to you, great, if not, I'll make a patch as part of the MSys2 build of Gambit.
Thanks,
Bill