This is not a good trend

As pizza mentions, no actual modification need happen to get different compilation or runtime outcomes.

Moreover, I believe the Fedora flatpak being different from the OBS flatpak is a red herring since the former is (if I understand correctly) not derived from the latter, but rather built from the OBS source, with a different flatpak runtime environment.

I don't disagree that it's a crummy situation and that Fedora should not distribute poor-quality packages which may be misconstrued as coming from upstream, but I don't see how it rises to a license violation, based on the facts presented.