Proton version will always work better if someone does not show an example and encourage the usage of native support. With Proton you are guaranteed to never reach the optimal potential, or get full advantages of the Linux/Wayland ecosystem. While with native versions you have at least the chance to get in there.
It is like judging someone for taking an advantage of the new CPU instructions that accelerate processing because general instructions are already good enough.
Native doesn't automatically mean better - quite a few examples of games running better on proton than with native executables(and yes then we can start arguing that it just means the native port is done poorly, but I'm just saying don't assume native will always run better).
It seems like a similar argument around the popularity of third party engines, whether studios should use Unreal, or whether they have the expertise/resources to change to and use another engine, or make their own bespoke engine, and if that will produce better results.
I think that is not fair comparison. Proton adds additional layer which can be completely removed and affects the runtime performance. Switching different game engine changes the layer implementation, instead of removing.
When Proton started to get good, there were multiple stories of small game studios just dropping their bespoke Linux builds because the Windows->Proton version ran much much faster and required zero effort from them.
