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That's because it's not actually an (extra) compatibility layer. It's literally just an open-source implementation of the APIs/ABIs used to support gaming on Windows.
While the implementation is different and may do things differently, the code doesn't fundamentally do more stuff.
I basically never run the native Linux versions anymore, Proton is always more stable and more performant.
I think that's actually Valve recommendations to developers as well: don't bother with the fast-moving and always breaking APIs and ABIs of native Linux support, just make sure your game works well with Proton.
It's insurance policy; an option. You can't do the work they have done over the past two decades to support Linux gaming overnight.
If Microsoft pulls some radical move, Valve will be in a better position to react than having to start from scratch.
It's a common misconception that Proton adds any overhead. It's just an alternative implementation. In some aspects it will be faster (and in some other probably slower) because the Linux kernel does things differently from the NT kernel.
I have not run any benchmark but I exclusive use Linux as my gaming platform. I don't play any multiplayer though and I think that's one aspect where Linux is behind. But for single-player stuff it's perfectly fine.
One thing though is that I have to filter out which games I buy by checking on ProtonDB their level of compatibility. But I can play major AAA games just fine.