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dnf vs packagekit updates: still unclear

Further to earlier help on this forum, I've been happily sticking to using terminal and dnf to update. I understood that gnome packagekit uses a different database and thus the possibility that later remove or uninstalls could mess up my libraries due to them using different databases.

So this morning I run my customary:

$ sudo dnf --refresh upgrade

Upgrade completes and I reboot (not strictly necessary perhaps, but an old habit). I then see a notification from Software Manager saying updates are ready.

Sometimes/often it is the case that this is simply an overlap, and that invoking Software manager again will refresh and show that "software is up to date". Today however, despite "clean all" and a complete refresh of the repos, followed by a restart, Software Manager is again showing updates. Clicking on it gives, for once, more explicit information. The updates are:

a patch to Firefox (Firefox was updated this morning with the dnf refresh but has not since found this patch); an update to Typing Booster, and - most problematic "OS Updates: Includes performance, stability and security improvements".

My question then is: what exactly is going on here? I was advised to stick to a single method for updates so as not to run into trouble with maintenance. According to dnf, after a complete clean and refresh, there's nothing to do, but Software manager wants to install unnamed system updates.

Is there something else I should be doing? Could I, for example, somehow simply mark everything as installed rather than mark individual packages? (this would be extraordinarily time consuming, assuming I could even find the list).

Are these sorts of basic conflict likely to continue? I understand that this is a rolling development but c'mon - conflicts between the core OS and desktop environment at this stage? Really? Would I be better off with Ubuntu or Opensuse instead? Perhaps I'm expecting too much of Fedora?

I'd like ONE, guaranteed, reliable and consistent method to ensure that things are kept orderly. I've now been running this install (number five) for about a month now with no major headaches! ;0)