My first thought is that this might be from having both Flathub and Fedora’s flatpak repo enabled together, “confusing” whatever math is being used to determine priorities/status/whatever.
Adding Fedora’s flatpak repo to my system does make Blender act like this. Disabling/removing it fixes the issue. My PC is not running Fedora but that is immaterial, for flatpak.
Is Flathub enabled by defualt in Fedora, now? When I was using it on my last laptop (38), I did have to enable it, since the Fedora flatpaks were not always the most current.