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.
Standard conversion of *.md, *.rst, *.pod, etc. to *.txt is IMO a plain bad
idea, because *.md, *.rst, *.pod files are meant to be readable text files
anyway.
Best wishes,
Guido van Steen