Yeah that would be nice. Some native Linux versions actually have worse performance than Proton when they're done poorly. I got ~60fps on the Linux version of Silksong, but 400fps running the Windows version through Proton.
That sounds like possibly a configuration issue rather than strictly performance (although I agree the symptom is worse performance). For instance, specifically the value "~60fps" vs something as high as 400fps sounds like running with vsync enabled vs. with it disabled.
It definitely is if you have an engine with a DX12 backend but no Vulkan backend. Nothing stops you from detecting Proton and then tweaking uses of the DX12 APIs that translate poorly to Vulkan, and there's no way adding a whole new rendering backend will be easier than writing the extra code paths in the DX12 one.