Most of Proton code is Wine. So basically if you have Wine in your system, library dependencies are not an issue anymore, apart from DLLs that some games require

If I have wine on my system and try to run steam-managed proton without any sort of runtime or container, 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, so your statement is false to begin with.

Why are they doing a fork instead of contributing?

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. They cannot contribute the entirety of proton to wine because wine does not want all their contributions. This is a very common situation to arise when someone wants to use an open source project but their goals don’t align.

But I expect it will be easier to push back on using containerization in Proton, than making Valve allow us such control

Valve is never going to rip out a solution that is working great for them and risk causing issues for customers for no good reason. Thinking that Valve are more likely to remove containerization than they are to allow you to modify the container is, frankly, delusional. It’s also completely irrelevant, as I’ve already said. If Valve wants to “fuck us up” then they’re going to do it. Steam is a proprietary piece of software that supports DRM for all your (also proprietary) games, which are stored on the cloud. You have no control over your games, but containers have nothing to do with it. And if they did, and Valve really wanted to pull a trick on us, asking them to remove the containers would make even less sense…