Initially I didn't like Fedora Flatpaks, but they have grown on me. What I really like about them is how they are built directly from Fedora RPMs.
Unlike Flathub, they don't pull and build dependencies directly off the internet (which may not get timely updates). Instead those dependencies come from Fedora's repos.
The way Fedora Flatpaks get built are also much more consistent since they just use Fedora's infrastructure. Meanwhile flatpaks on Flathub may be repackaged Appimages, snaps, tar.gzs, built from source, etc.
Though there is the obvious downside of Fedora Flatpaks which is missing media codecs. So if an app needs codecs, I just end up using Flathub versions. And Flathub for whatever isn't in the Fedora Flatpaks repo.
I did start trying to prefer the Fedora flatpaks but the flatpak priority system doesn't seem to work. I have flathub 50 and Fedora 100 but it still chose flathub for the same version.
Flathub's packages are usually more up-to-date. Sometimes ridiculously different.
Then LibreOffice said that they're releasing on flathub/fedora not packaging so eventually I saw which way things are going and went with the flow.