Linux

then I’m running proton on different versions of libraries than the ones it was compiled for and tested on. Proton also has additional components which might mean additional dependencies

We are slowly getting to the end of my depth in Wine. But in all the years of watching various Wine bugs and enhancements, I have never seen something blocked by the version of library or because some OS does not have, for example, current standard library updated. Kernel version, sure, but that's much less a compatibility problem. Hence, as long as Wine compiled and is available on your system, from the game perspective, the only libs you have to worry about are Windows DLLs or Wine built-ins of those

The fork is open source. As far as I know, some contributions do get merged into wine. Valve is also funding work from Collabora which is contributed directly into wine

For now. I'm sure they would love to get into the position that console companies and Microsoft with its DirectX had. "You want to ensure your game works on the new gen? Here's the paywalled support for our closed-source thing".
If they haven't started already, I expect them to come up with their own, closed sourced implementation in a few years/when they gain enough market

Thinking that Valve are more likely to remove containerization than they are to allow you to modify the container is, frankly, delusional

Boycotting their containerization might be doable. Forcing them to make their containerization configurable much less so