The colors on my Deck are inverted but oddly only in select places since the 3.5 update
The update boot screen and the desktop wallpaper and icons ONLY in Nested Desktop, everything else from Steam's UI in Game Mode, Boot Videos, actually in-game, the desktop in standard Desktop Mode, and the taskbar/start menu/all apps/etc in both normal and Nested are the correct colors (as shown by the last screenshot)