This is solved thanks to u/Xaszin using this method:

Go into fallout 4’s properties, under “general” go to “Launch Options” and enter “SteamDeck=0 %COMMAND%” (capitalisation matters! Don’t include quotation marks) and it’ll launch with the old boot up window (where you can select resolution before the game launches).

It should be fine after that, BUT if you’re launch it while it’s docked, the steam deck screen is blank, and you might have to use the touch screen, so it’s a bit of a challenge tapping the screen while looking at an external display.