I'm looking at you, ubisoft
Reason for this meme is that some ubisoft titles are shipped with a broken version of ubisoft connect launcher. Installing these games is only possible by running the installer for the launcher again via protontricks.
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Well, not exactly to be honest. You'll still have a lot more problems than gaming on Windows due to fragmentation.
But, if your distribution system is purely flatpak, then yes, it should be smooth.
You're right. It's just frustrating that most games could run better (or at all) if publishers paid just a little bit of attention.