A change that Valve missed in the big recent upgrade of the Steam client, is that on Linux systems either desktop or Steam Deck, removing non-Steam apps should now be cleaner.
Previously, if you added something into Steam that ended up making a shader cache and compatibility data, like running something with Proton, when you removed the shortcut from Steam it would leave everything behind. That should no longer be the case, as Valve developer Pierre-Loup Griffais mentioned on Twitter:
Linux change we forgot to call out in the new client: removing non-Steam apps now properly removes all related files like shader caches and compatibility data (which would previously be left as 'other' storage space)
So people can eventually stop asking "What's taking up all my "Other" storage?!", which has been an ongoing problem since the Steam Deck's release and especially a problem on the 64GB Steam Deck model.
Even though Valve don't actually support non-Steam apps directly, it's nice to see them make steps to make the experience better.