You've now got conflicting requirements. Can you step back and specify what you want, instead of potshotting at the solutions because it's what you don't want?

If you want pod tools that have an ifdef, you'll need to write them.

If you want existing pod tools to work, you'll need to code your internal stuff as non-POD.

There's no "third solution".

-- Randal L. Schwartz, Perl hacker