No trademarks in upstream source

Wol, please cite the exact license text (and context/location in the license)

The only things I find in GPLv3, GPLv2, & LGPLv2.1 are:
* In the preamble, it says modified versions should be clearly identified so the original author isn't besmirched. It then says the exact terms are specified later, so while there's an intent there, it's not (as I read it) the binding text
* Later it says that the *sources* must be marked as modified and when (but not how)
* License must be clearly marked
* Original source must be clearly marked if in a combined work
* GPLv3 does allow you to add licence terms to strengthen this further, but it's not the default.

There is nothing about "must mark the resulting version as your own"—just that it must be clear what the license is (so they know they can request source) and then that source must make the modification clear.

I dunno about flatpaks, but assuming there's some way to track them back to their sources/build recipes, then it should be clear they're based on the RPM.

RPM versions inherently identify themselves as distinct from the upstream version (due to the RPM release version added) so that format plus its storage in Git by the Fedora project addresses all the license terms of use (or should).

I didn't read the terms exhaustively, so if I missed something, please point it out.

You've also filed a bug, I assume? From what I've seen, the project takes licensing extremely seriously (they've done intensive license audits, catching numerous violations and defective licenses that other distributions missed)