Yeah, I even completely overread the info below the config settings. It's just unusual to have two settings for it, so I never gave it a second thought or look. Combining them to one switch or maybe a popup info to the player after they changed one of them about the other one would make this bulletproof.
Or I'll just try to remember this the next time I play the game, because I will. It's great work so far. Well done.
Edit: I almost forgot. There are some bugs with the Map (Exterior Space Ship view).
If you have the map open and right click instead of opening the SD menu or closing the map the free roam room you are currently in is shown with the map still in the background.
Also, when you press escape while in map mode, the main menu opens up with a crazy flickering map in the background.
And if you load a save file while in map mode, the map stays open in the background even while not in free roam mode and just like described above, when right clicking, the map shows up instead of the SD menu with the SD icon in the bottom left staying absent while in story mode.