It was quite recently reported again that Module::Build still hates PREFIX= (despite it having been quite a while since the last time I heard rumor of somebody going to teach its author how to handle PREFIX= in a reasonable way). Perhaps the report is due to an old version of the module being used, but I suspect not. (And, yes, "perl Makefile.PL" 'should' work even if Module::Build was used, that is, so long as you don't specify PREFIX=.)

Of course, I don't have to strain at all to imagine cases where "cp -pr ..." would fail.