I was able to get a very minimal/blank 5.0.3 project to work on the SteamDeck following the guide at How to load and run games on Steam Deck (Steamworks Documentation)
I haven’t had a chance to test the “Launch” option mentioned in Steam Deck Quick Start in Unreal Engine | Unreal Engine 5.1 Documentation yet because it was broken for 5.0, but it looks like the change to fix it was released in 5.1.