I’ve activated automatic updates in Gnome Software Center. Now more and more updates are shown to me here. Even after a reboot, the update notifications are still there.
If I manually click on “update all” and reboot, the update notifications disappear, but I actually thought, after reading the documentation, that updates would require no action from me at all, and that’s what I want.
The weird thing is, the installed programs themselves claim to already be on the new, updated version.
So why are the updates still shown in the Software Center?
You are using Firefox installed through flatpak, but the base image also contains Firefox. Even if you remove it with rpm-ostree override remove it will continue be showed in the list of updates. I’m not sure for GNOME Software because I don’t use it. And what is for Signal, maybe it’s a GNOME Software issue.