Yes, that first pragraph is (sadly?) my experience too. Almost every game that have native version was somehow worse than windows version with proton. Black mesa gave me all sorts of weird glitchy light effects, Pillars of Eternity only ran at 60 FPS and had half of the fonts unreadably blurry, the other game (forgot the name) lacked plenty of updates on linux, etc. And all these problems went away with proton. Is it sad? Yes. Do I care much? Not really as long as proton is hassle free.