I don’t remember exactly but yeah you are probably right. I think specific games needed it because they wouldn’tlaunch otherwise. I run a bunch of gog games out of the same bottle just because I don’t like having to create a new prefix in heroic. I make back ups before installing every game but its working fine with no issues.
Like I said, I have little experience with flatpak version of bottles so I can only say I’m experienced with the AUR package. If you’re having troubles with flatpak, I doubt switching to AUR will change your experience very much.