Update: there seems to be a misunderstanding of the question: I'm interested not how to do that myself, but how to teach module X to interact with CPAN in automated (3rd user)/controlled (CPAN testers) environment.

Once Makefile.PL runs, I'm pretty sure you can't get CPAN to automatically run it again after a prerequisite installs. Instead, you need to find a way to have the necessary configuration done during the "make" stage. I can see two ways of doing that:

1. Override ExtUtils::MakeMaker methods to change the generated Makefile such that during "make" you gather and use some configuration data. (Hard)
2. Use another *.PL file and the PL_FILES argument in Makefile.PL to either generate a module with the information from your prerequisite or to patch your .pm files in blib as necessary. (Easier)

Alternatively, you might look into using Module::Build, as it makes subclassing Module::Build and overriding methods fairly easy. You could override the ACTION_build method to gather necessary information, act on it, then call the superclass method to continue the build process.