Not a pure Perl mechanism, but your local packaging mechanism might support automatically applying patches on build to a stock source tree (specifically I'm thinking BSD-y ports, but I'm pretty sure RPM provides something similar and would be surprised if apt/dpkg didn't as well). You could make local packages which pull the official source and then apply your patch in the build/install. That'd also give you the benefit of having the modules under package system control.

(Granted I'm iffy on doing this with macports myself versus installing straight from CPAN, but thought I'd throw the idea out.)