Linux native for me was always somewhat problematic in the past. Frankly if someone tells you otherwise they’re lying. Proton makes the process simple, click install and play, that’s it, and that’s all any consumer needs to do.
The only long term consequence I can see is if Microsoft decides to make using compatibility layers for their SDK’s intentionally difficult or downright illegal. Valve so far has proven as long as they can do it, they’ll update proton to make games work. The question is will someone pick up the torch if valve eventually stops?
I treat them the same, doesn’t matter to me as proton really is performance parity with Windows and that’s really the baseline.
Until porting natively is just as easy as using proton, no one will port natively. At this point who cares? Native and proton to me are the same at this point.