I think that your example of the App Store and the Microsoft Store is helpful! I work on both systems at my job fixing computers for consumers. The only thing I dislike about the App Store is that it doesn’t let you install things without first signing in with an Apple ID (the spam levels of pop-up messages trying so freaking hard to make you sign in is infuriating). But the MS Store feels like all the worst parts of the Play Store and really fucks things up if it breaks. I will likely remember your reply the next time I think about Flatpaks and Snaps though. lol
It might not be the answer, but I have had some games do very weird shit in the past (AMD GPU as well but on Windows). I found out that some games really don’t like if you have applied AMD settings that override the game’s graphical settings. Do you just have the AMD kernel driver, or have you installed the one with the Adrenalin from the AMD site? If you installed the Adrenalin software, you might want to try setting all the options for the game to only use game settings and not allow the AMD software to take over. If it is the one that ships with the kernel, then I am not sure how to change stuff that might be trying to override the game. Maybe see if there is a Proton version that might be better?