The man page for fedpkg, as shipped by Fedora, contains a double %%:

[…]
COMMAND OVERVIEW
[…]
       fedpkg verify-files [-h] [--builddir BUILDDIR] [--buildrootdir BUILDROOTDIR] [--arch ARCH] [--define DEFINE] ...
              Locally verify %%files section
[…]

Glancing at the code, pyrpkg/man_gen.py appears to invoke argparse's format_help() and I'm not sure whether that call should return a string with the expanded text (i. e., %% transformed to %) and if it does. But in the end, the generated man page should only contain a single %.