Here’s a potentially unpopular opinion… Games that target the Proton API are actually native Linux games. Proton isn’t virtualization or emulation, it’s just an API that happens to be mostly compatible on both Windows and Linux. Other than the kernel itself, Linux has never had one true API to do anything… there’s always more than one option to target (as you note with your Wayland/x11 example, but also pulse, alsa, pipewire, the list is endless). Proton is an API that’s available on Linux, and programs that target the Proton API are Linux programs in every way that matters.
The question isn’t native vs proton. The question is whether proton is a good API. At the moment, it’s an API that offers pretty good cross platform compatibility with windows, which is hugely valuable to developers and they’re using Proton for that reason and even testing against it. That’s good for us as users and for gaming on Linux.
If Windows evolves their versions of the proton APIs in ways that break compatibility and are difficult to fix, we may find that game devs complain on our behalf to avoid breaking their Linux builds. If Proton begins to suck compared to alternatives, and enough people are playing games on Linux with Proton, devs will organically start to look at other porting options more seriously. But Proton is both a way to kickstart the chicken/egg problem, and itself may just actually be a good API to develop Linux games against.