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.
This seems like it'd be useful for people who install game launchers like Battle.net through Steam, although I am assuming more care needs to be taken with the instructions now otherwise you might accidentally delete your install. I'll have to test this feature out soon.
This is great news, I've been playing D2 : Resurrected on my deck, so I definitely fall into the category of folks that install non-steam games that use Proton.