The idea behind it is really for corporate uses of Fedora/GNOME. Sysadmins, through Fedora Flatpack, can re-package certain software from Flathub in accordance with their draconian corporate policies.
As a person that has had to endure stupid corporate policies and since Fedora is _mostly_ used in corporate workstation. I can understand this.
What I don't understand why it's the _default_ to prefer Fedora Flatpack software over Flathub. For people that are just getting into linux, I can see why that's painful and the UX to be terrible.
"I installed Z software. It installed some junk re-package. I only realized it installed junk re-package after a week of investigation. Installing it from different source and now it works. Thanks, Fedora! I wasted a week of my time!"
Also, distributions can also provide their flatpak repos (or even another third party) and vet the packages with their own set of rules (such as "no packages with full filesystem access").
Fedora has its own Flatpak repo as the default instead of Flathub (which has the official OBS package from the upstream developers).