You give a good description but I think the key lies in some of the details that you have (reasonably) omitted. If I ran into this problem, I'd use

   % perl -d Makefile.PL PREFIX=/my/perl/dir
  DB<1> require ExtUtils::MM_Unix
  DB<2> b ExtUtils::MM_Unix::init_main
  DB<3> c
[download]

and then step through that subroutine in rather large chunks, watching how $self->{INSTALLPRIVLIB} (for example) gets manipulated as it goes along, figuring out why $self->{PREFIX} does not end up affecting it.

The code that does this is complex enough that I didn't see any hope of me spotting the problem without concrete details about your Config.pm file settings, etc.

                - tye