I think it opens the door for failures. A shared module shouldn't really be shared. Sure you have multiple copies (probably because you are a developer), but real users are unlikely to have multiple copies.
Btw how about XaAES? I hope that you still plan to keep the current xaloader behavior, i.e. loading xaaesXXX.km depending on the build. If this is the case, I guess we could live with machdir = sysdir, as I'd define GEM=/c/mint/1-19-cur/xaaes/xaloader.prg and nothing would be duplicated.
We've got two different goals here -- mine is to have multiple architectures with as little duplication as possible and yours is to have mach-only based kernel, modules etc. Now I think about someone who does *not* want to have multiple architectures... wouldn't be strange to have only c:/mint/1-19-cur/ara (with empty c:/mint/1-19-cur) ?