What does :make buy you here? vim's makeprg just automates loading the error file, but that's taken care of in the Prove function. If you're going into the trouble of using make IMHO you may as well leave it for c development so that if you're writing a module with XS in it you get quickfix benefits for that.

Did you figure out that CompilerSet business going on in compiler/perl.vim? Maybe that's the key to localizing settigns that will help develop with more than one language at a time.