It’s a Linux pc.. so top notch Linux support I’m assuming is part of it. Plus it has a kind different control system and whatever graphics and sound it has as well.
There were claims that Valve asked some developers to remove their Linux "native" versions of the game since the Proton version is better since the devs didn't support the "native" version very well.
Allowing developers to outsource the work for supporting Linux makes game developer's jobs much easier.
That doesn't contradict what they said, it reinforces it even:
> Really, it comes down to whatever is the best experience. So if it's easier for the developer to get to a point where the best experience is achieved through Proton we think that's great
Asking some developers to remove a native version of their game is not the same as asking all developers to target Proton. If anything it's more an indictment of those specific dev's ability to target native Linux.