Fallout 4 just got updated with a “next-gen” update that got the game Steam Deck verified, fixed bugs, and added some new content.
However one of the ways they got the game verified was by disabling the game’s launcher by default, the same launcher that is the only way to change graphical settings.
You can re-enable the launcher by changing your steam launch settings to SteamDeck=0 %command%
Totally not needed either. Just have an additional shortcut for “safe mode” and it’s fine. No need for a full launcher just for that…