Hi Jerome,
I may not fully understand the issue, but why not keep *.md, *.rst, *.pod, etc. the way they are?
The main advantage of *.md, *.rst, *.pod, etc. is their readability. Their additional advantage is that they can easily be transferred into *.html or many other formats, if desired.
A missing man page might make such a conversion necessary. In that case a *.md, *.rst, *.pod, or a .whatever file could be converted into *.*roff, which should be done during build process.