I guess it never was.

So Fedora auto-converts all its apps to Flatpak. Does it at least namespace them to something specific to Fedora?

No, it doesn’t. Fedora publishes its Flatpak of GIMP as org.gimp.GIMP. This conflicts with the official org.gimp.GIMP published by the GIMP developers on Flathub. On a fresh install of Fedora 34, if you add the Flathub repository and type flatpak install org.gimp.GIMP, you get prompted for which one to install:

[nick@fedora active]$ flatpak install org.gimp.GIMP
Looking for matches…
Remotes found with refs similar to ‘org.gimp.GIMP’:

1) ‘fedora’ (system)
2) ‘flathub’ (system)

Which do you want to use (0 to abort)? [0-2]:

If you choose option 1, you get a build of GIMP with Fedora’s patches that uses the 650 MB Fedora 35 runtime. If you choose option 2, you get a different build of GIMP that uses the 1.8 GB freedesktop.org GNOME runtime.

There's also a recent post on the GNOME blog debunking some of the claims (for specific environments):

https://blogs.gnome.org/wjjt/2021/11/24/on-flatpak-disk-usage-and-deduplication/