I would really prefer native if there is the opportunity

I prefer native apps too, but I'll still use websites and some electron apps, and I'll still use applications built in C#, Java, Python, etc. None of those are really native either. Proton is analogous to a virtual environment for running an interpreter. Potentially, it's slower and has issues a la Python, but if the program can work, then I don't care about the theoretical problems; it works despite them. So I think it's fine.

If it means more games for Linux and a standard that developers can target, encouraging them to "support Linux," then that's a win I think. Like I said in another comment, a studio can buy a steam deck, throw the same Windows export on it, and then have someone run through the same set of tests they'd normally go through. If it works there, it'll work on most Linux machines. Having a standard API is not a bad thing imo