If a new user installs malware from flathub while trying out mint for the first time, they’ll probably blame mint instead of flathub. Nobody will say “damn, I should have listened to that warning” while their “discrod” app rm -rf’s their entire PC away, they’ll instead claim Linux is crap and go somewhere else. Doing this helps keep mint safe, and definitely encourages unverified FOSS apps to hurry up and get verified.
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).