The Steam Deck OLED is still pretty new, it could be the Proton compatibility layer needs an update for the game to be able to detect the HDR screen. I'd say give it a bit of time, but I'm not sure if it's even Rare that's working actively on the Steam Deck support, to be honest.
Astralenigma
Marauder
X-Box and PC use similar code since it's mostly Microsoft software, Steam Deck on the other hand is Linux which runs Windows games through Proton so as RealStyli said it's more of a Steam/Linux/Proton problem than a Sea of Thieves problem.
