Support for Steam Deck != support for Linux version.
You are correct , however proton ( and the upstream project wine ) is made for linux not the steam deck , ie a game which works on the steam deck will work on linux in most cases .
proton / wine can also be used to run a lot of non game software made for windows ( though proton is made explicitly for games ) , though I will admit steam has the best ux around running software using wine or proton .
but yes it is a Tim Sweeney problem , not a Linux problem .
something I will also add is that they have at least part of the game running on linux already , unless they are paying a fortune in both licencing and lost performance by running the games servers on windows .