Proton is basically wine + dxvk + esync/fsync/wait_v with some community patches (e.g. using a "fake" fullscreen mode that scales up to native res rather than switching resolutions explicitly) and integration for e.g. steam input handler.
In other words they're bundling up a bunch of open source tech with sane configuration and adding a few steam integration patches. And it's all open source, on github, too. There isn't much that Valve does explicitly in regards to what windows APIs are supported, and what they do develop and fix gets submitted to upstream wine (though not everything is accepted, I guess).
I suppose, if Proton usage explodes such that the bulk of patches to wine get submitted by Valve devs, what you said would be true, but so far that isn't really the case.