I don't disagree with most of that, but none of what you said actually addresses the problem. The problem is that there are functionally two (notable) flatpak repositories, but one of those is going against the will of the upstream software devs and shipping broken software that they have asked them to stop packaging. And Fedora users are getting the broken flathub repository as the default, without really having reason to suspect that their "flathub store" would ever trick them into installing from a different source. The "verified" badge, especially the lack thereof, does not address that.

As for users feeling “tricked”? That’s a difficult thing to say. I would like to say that users should at least know something about the distro they are choosing (ie Ubuntu users should know about snap; Fedora/Debian users should know about their stances on FOSS, security, and patents; Arch users should know its a DIY distro).

You can RTFM someone all day, but if you actually want Linux to be adopted by more people, you need to reduce the anti-patterns. Snaps are generally known about because they are infamous for also breaking packages. And they're still major footguns when people are recommending Ubuntu to people that are new to Linux, who are the least likely to know that their apt package installations are going to be installing differently-packaged software that has its own set of problems. If we get to a point where Flatpaks have a similar problem to Snaps, we've taken a wrong turn, and it will only hurt Linux adoption.