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Centralization is not a good thing IMO. Im glad Fedora is bothering to maintain their own repo no matter how useless we find it.
What is good is users having a choice, but Fedora Flatpaks are the default choice and users have no way to change it. Many don't even realize they are using them instead of the official ones from Flathub.
Users actually do have the option to change it, you can change both the order, disable their own flatpak repo and decide if you want rpm or flatpak as the default source. If you do disable their flatpak repo the warning shown in the OP disappears:
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TIL that Discover let's you change it. AFAIK there's no way in Gnome Software though
Ah, I haven't looked into disabling Fedora Flatpaks in GNOME Software. A quick search only returns how to remove it all together and not sure how the GNOME Software reacts to doing that.
WARNING - THIS WILL REMOVE ANY FLATPAKS INSTALLED FROM FEDORA FLATPAKS