Mission Trees that extend to the right are cut off. Either get the Steam Deck Mission Trees mod from (currently until the Steam Workshop is activated) Paradox's mod site (disclaimer, I am the author) OR set the UI scaling set to 0.8. That's if you want to keep 1280x800 res, otherwise go to 1920x1080. Also the empire selection screen does not spawn the selection cards at 1280x800. Use the before mentioned UI scaling or resolution fixes, start your game, save, and if you want to reset your fix, you can and keep your empire.