Usually I am also oldschool, a thousand years I ignored all of this stuff as I come from server environments. I really don't like all these things, because you don't have a single point of responsibility and liability. That is why I don't like to work with pip and npm and how all these are called and started to move to compiler languages without thousands of different dependencies and package managers. Another story is systemd, never been a friend of it, the simple fact that logs are stored into binary files is a sin in my eyes.
It's is only that I used Flatpak because it is the first serious time I started to use Linux for Desktop. I will now remove that and move to APT/native packages and then have a look if the problems persist
As you do, I am going to slink off to bed and hide under the blankets. It just turned 4am and I meant to slip into a coma hours ago...
EDIT: By the way, keep the X-Swat updates and 6.7 kernel if they are working error free for now, due to your 4070 card.
They may help for the other graphical glitches you had.
are gone after I changed the DisplayPort 1.2 cable to a DisplayPort 1.4 cable from the same manufacturer. Seems 1.2 may have problems with modern 165 Hz monitors.
The fullscreen bug though remains. I did not yet update the kernel because I first wanted to test the new cable.