The prefixes should be loaded from the Makefile when cross-compiling, which we detect from _PYTHON_PROJECT_BASE being set, which should be the case in make test.

Does sys.base_prefix ever differ from the Makefile value? I am not entirely sure how the Python "installation" works on Emscripten's virtual file system. Can it be present/mounted/installed(?) on a directory other than the one specified in the Makefile? If so, and if that's where this problem stems from, then this isn't an issue specific to Emscripten, but rather all relocatable installations, which is something this test currently does not account for, but it probably should. If this is the problem, then I'd prefer to fix the underlying issue rather than special-case Emscripten.

I think I found the problem.

Opened #128556 with an actual fix.