From the couple of games where I’ve been able to compare; frames per second are exactly the same, but the CPU runs a great deal less hot. No concern on desktop, but that would make a difference on the Steam deck.

(Mark Of The Ninja has a deadlocking issue on native that it doesn’t have on proton, got quite a few of Frictional’s games - Penumbra, Amnesia - that just won’t open on my main monitor when native, and most recently Silksong has been really funny about my 8bitdo controller when native. Works great with my fightstick, though.)