Interesting behaviour: When downloading and opening a .flatpakref file in GNOME Software, it offers to install the flatpak from the remote fedora instead of the one referenced in the .flatpakref file. I could just observe it with the org.gimp.GIMP which is 3.0.0 in flathub but 3.0.0RC3 in fedora.
If someone reads this and can tell me where to report this I'd report it as a bug as it's unexpected behaviour.
@fluchtkapsel definitely needs debugging; open an issue at: https://gitlab.gnome.org/GNOME/gnome-software/-/issues/new
Also attach the flatpakref file.