If this is a reasonable approach, what are the recommendations? Should this be done in Makefile.PL somehow? Should there be a conf file that is provided and ask the user to modify that if they want changes? How should that be incorporated?

File::HomeDir + File::ShareDir => File::UserConfig

You can http://search.cpan.org/perldoc/ExtUtils::MakeMaker#PL_FILES to generate sharedir/ThisMachineDefaults

Then in your module/program use File::UserConfig, so users get an .appdir with ThisMachineDefaults copied into it, which they can customize ...