This comes from two things:

• fedora-third-party enable/disable create and remove Flatpak repositories rather than enabling and disabling existing repositories. (*)
• The toggle in the Software Repositories dialog does not affect existing repositories, but only ones that are added in the future (it runs 'fedora-third-party enable/disable --config-only`) Existing repositories are meant to be handled by the user one by one.

There are basically two ways I can see to fix this:

1. Make the handling of flatpak repositories in fedora-third-party more like that of dnf repositories - they are added via the system mechanism - in the Flatpak case dropping a file into /etc/flatpak/remotes.d/ - and then fedora-third-party only handles enabling and disabling them. This requires a Flatpak change to allow having a disabled entry in /etc/flatpak/remotes.d/.
2. Make fedora-third-party still handle adding the remotes, but when gnome-initial-setup or gnome-software records the user opting-out by running 'fedora-third-party disable', have it run:
   flatpak-remote add --disable --from /usr/lib/fedora-third-party/conf.d/fedora-flathub.flatpakrepo
   So that we get a disabled entry that can then be enabled through the gnome software dialog.

Approach 1. is clearly better than 2., but 2. is probably the only feasible solution at this point for Fedora 36. I don't see an issue with doing 2. for Fedora 36, and doing 1. later.

(*) this was done to match the way that the GNOME Software repositories dialog used to be, when there was no enable/disable for Flatpak repositories - but then the repositories dialog was changed.

Created a new flatpak-module-utils build that should fix this for new installs, can't do anything about existing installs:

https://bodhi.fedoraproject.org/updates/FEDORA-2022-f2efc42252

Thanks Owen! That will have to suffice.

I've added a new update: https://bodhi.fedoraproject.org/updates/FEDORA-2022-1ed936a3ac that should improves things for existing installs.

If a system opted-out from fedora-third-party when installed or upgraded to F35, then a disabled "Fedora Flathub Selections" remote should now be added on upgrade. (If the user opted-out then changed that to opt-in, then an enabled remote will be added.)