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Afaik yes, the token is keyed to a specific source in the case of verifying through a website, but from what I can tell, that doesn’t stop someone else from creating a separate malicious website (or git repo) that looks similar but contains malware, and publishing that as a verified app with a similar name as the real app to flathub (so there would be multiple versions of an app, with only 1 being the “real” one on flathub).
That’s why they’re not separate distros from Fedora (as in, they don’t even host their own RPM repos nor maintain their own set of Fedora packages like Manjaro vs Arch) and purposefully so. It’s just stock Fedora with a few configs, third party repos/packages, and some scripts preinstalled. The entire thing runs on GH actions.