The FUD about MakeMaker is just as bad. Your assumption that we haven't read the docs, or that we'd magically agree with you when we did, is similarly disheartening.

I'm not sure why you think you have to make Module::Build's PREFIX do the same thing that MakeMaker does: just make it do something that will work for the users if they specify that option. As long as perl can find everything most everyone won't care will things end up. To me, that's the big design mistake no one wants to fix.