Comment # 1 on bug 1012272 from Dominique Leuenberger

That's pretty much the same as bug 941862

EVen though that bug is about RPM files, the main component missing is the
.desktop file (which we don't ship due to it not working with our PK backend
for now) - The handler might already work for flatpak; but last time I tried
it, stupidly enough PK was still being queried - needless to say it failed.

Might be worthy to re-check and possibly install the handler only for .flatpak
and .flatrepo files (skip RPM until the underlying PK issue is fixed)