Which Nvidia driver setup do you use? The problems arise with the proprietary driver; if you roll back or use a different kernel than the current default (as specified by the repo) both my brother and I had the unfortunate situation of the driver kernel module missing. Nouveau or NVK probably don’t cause such issues.
Like I said it’s less of a problem with KDE, they even got a button to add Flathub specifically in Discover. It’s more of a thing with Gnome and Gnome Software where no “Add Flathub” button exists (and also no GUI to add repos -> they have to look up the whole CLI command), so newer users won’t necessarily be aware that something rather important is missing.