KeepassXC should just work, if the browser's key was added to your KDBX database successfully. Other than that, I am surprised.
Yup, the motherboard clock thingy is a consequence of Windows storing local time, vs Linux storing UTC. It's a minor thing to fix in any of these systems, though.
Shortcuts thingy - never had a problem, although I did have a problem with KDE's keyboard shortcuts to run a program, which may be related workflow and maybe both were/are broken.
KDE Connect is surprising, as at least for me it worked flawlessly
The reboot thingy must be related to Linux Mint. I saw similar thing in EndeavourOS. One nice thing that some distributions implemented, is the ability to apply updates when you poweroff - from my point of view it's a less annoying solution than what you describe.
I can't comment on the 'cherry on top' one without more details.
I had a somewhat similar issue on my work laptop a short while ago, when I installed a program, which included a bugged XML settings file, then ran system update. When the updater tried to rebuild some caches (related to ie. icons, MIME etc.), some programs which use these caches simply stopped working. Reinstalling all packages with apt was the only thing that helped, to this day I do not even know all of the parts of my system that were broken.
But this was one of these issues that happen once per 5 years, and leave you scratching your head and asking "what the hell is going on here?". The difference from Windows is that in Linux, you can have a high understanding of system's internal modular components (at the cost of time needed to learn it), and regular system issues can be identified after a few minutes of Googling.