Hello and welcome to the forums. I first thought not to answer but now concluded perhaps giving a better insight may help for a better understanding also: When I as a user need first to configure a repository NOT to transmit non-free (or foremost non-free) software, then this repository has one elementary first issue as it does not clearly transmit free software but is somewhat vague and mixed. Hyperbola as system does not include such software, besides we also do not incluce flatpak as we decline package-management aside: It bears - as already mentioned here in the thread - the risk of unknown licensed software being installed and the user has neither a chance to look into nor is presented the details. This leads up to the point that people / users / developers do no longer really care of a software being free (clearly) or more vague or even worse.

Besides all that flatpak itself does not present other repositories and only their main one first. So also here: If I need first to replace that or modify it afterwards further, the software itself does not leave a clear choice and is not presenting that to me as user. Further more and more projects conclude flatpak as prioritized way of distribution, which is leaving the question: Who in fact cared most of backporting and patching? The point is clear as upstream only does updates but not often backports. That work, including further modifications, is done by system-distributions and upstream also does not care really about distributions going on. Focus only are the bigger ones, not small projects. That's out of the same reasoning why Hyperbola does not bother with such packages like flatpak.

Hope that clarifies a bit more and help.