You probably already know but just in case, xournal++ is a good alternative I've been using. Not quite as feature rich but does all the basics. Linux on a windows tablet is a surprisingly usable experience, if a little janky.
Don't get me started on ds9. A black captain? A trans lesbian officer? A gay interspecies couple? The federation using fear from war as an excuse to become a police state? Can't believe they made my colorful space communism show woke.
People are right about flatpak - it will generally keep stuff out of your actual root/home directory. But like you implied, the steam flatpak is unofficial so you may run into issues. With that said, I've used it and know many people who use it without any problems.
And depending on the game, you might be able to run it directly with steam offline, or even straight from the executable without steam open at all.
Of course this isn't airtight, but there are ways to check the permissions granted to flatpak applications. And IMO it works well enough for games. Ofc this depends on how paranoid you are and your reasons for wanting this (fear of a game being a virus, not wanting clutter in home, wanting protection from a bug that would delete data, etc.).
I had issues with debian-based distros as well, that's why I switched to fedora. I also think the go 3 has better support in general. The cameras are still annoying but things have gotten better, with Firefox getting libcamera support.
I personally got a surface go 3. Put fedora on it and the surface kernel and it works pretty good - GNOME's interface honestly works better for touchscreens then windows. Just be aware that some config might be needed - I had an issue with the keyboard that required making a udev rule (I documented it on the surface kernel github issues page).
I use it in a similar way keep track of homework, linking to the assignment since I have almost no assignments that aren't online.