Why separate it out? The POD tools should have no trouble finding =pod ... =end blocks within any kind of text file.
To hide it from C, use #if 0 / #endif, not comments. Then you don't have to worry about any stray */ characters or C comments within the documentation.
I understand your concern about indenting. Why are your functions indented in the file? Or do you mean you are putting POD within functions?
Having a pre-indent for everything makes it harder to ensure that normal paragraphs are at the right level as distinct from verbatim paragraphs which are indented more than that pre-set. I think you are asking for trouble, unless you come up with a more comprehensive approach.
If nobody has such a thing already, I suppose you will be designing it. I look forward to that thread!
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