I don't think this is as much of an issue as you are making it out to be. I have my Steam Deck on the main branch release which seems to exclude it from downloading precompiled shaders. When a game updates it has to compile the shaders first, but even on a big game this does not take an unreasonable amount of time. Less time than it takes for game updates to download at least.
Steam could improve the experience here by having the shaders compile overnight in the background so it presents zero delay but the current way doesn't bother me much at all.