Cool idea. I suggest you use the =begin or =for directives for the purpose; you could then f.ex write =for autodoc and follow either a regular paragraph of POD or maybe a line of autodoc-specific commands. All other current POD parsers will ignore =for and =begin sections addressed at other parsers.

A good place to start might be the Pod::Simple documentation, which includes a perlpodspec POD.

Makeshifts last the longest.