The OBS Studio open-source screencasting and streaming app has called out Fedora's poor Flatpak packaging of the application and is threatening as going as far as legal action if it isn't addressed.
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:
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
Honestly they should make it closer to F-droid. They already have only Foss software on it now all they need to do is implement strong privacy and security rules.