Cons has been talking for a long time about moving to an architecture like you're describing--a modular build engine to manage dependencies, with plug-in modules for various dependency scanners, compile tools, etc. The consensus among that community is that itwould be a Good Thing, but no one has actually had time or energy to go ahead and do it.

I agree completely about the hassles arising from Make.pm being so closely tied to Make's syntax.

I'm not sure what you want to do in Perl that you couldn't do within a Cons config file itself, since it's just a Perl script. You shouldn't need to do a separate system("cons $foo").