Someone on reddit said they played the Stadia version and had the controller UI and said it was great. Frankly, if it's like DOS2, then you'll be fine. However, it's likely to be much better since Larian said they're going out of their way to support stuff like the Steam Deck so they're likely to make tuned controller schemes specifically for the Deck.
However, I'd imagine the typical controller scheme would work just fine too even if you miss out on some of the Deck's features and buttons. You could always map those yourself. I wouldn't worry.