I was playing Project: Gorgon recently, I was about to refund because it ran terribly on my machine (despite the low end graphics), when I noticed it was using the native build, switched to Proton and got a 200% FPS boost.
As long as I can play on Linux, I don't care what translation layer it goes through.
Among many game developer studios, the Steamdeck is increasingly becoming the defacto low-spec hardware target. Running their game on a Steamdeck becomes a core part of the QA process, because there's a few million Steamdecks out there actively playing games, and if your game runs on a Steamdeck you basically know it'll also run on a very wide range of hardware configs.
So while the game might be targeting a different API than the standard ones exposed on Linux machines, a lot of games now are directly designing their software to make sure they run well on a Linux handheld. Meanwhile, Linux is adopting more and more features to better support this non-standard API set.
At a certain point I think we can just call Proton/WINE a 'native' API for gaming on Linux, and say that games developed with Proton/WINE in mind are native games.
Perhaps we're not at that point yet, but we might be there soon.
In fact, I went with console + linux laptop for ages simply because that combo excelled at their respective roles, were cheaper together than a gaming pc, and it 'just worked'.
I did eventually cave and build another gaming pc, but that was after I acknowledged that I could push out on the price / perf curve to something less 'optimal' (and it let me play with local LLMs)