The problem is here: https://github.com/MennoMax/the-hungry-magician-game-jam/blob/master/settings.gd...
You are creating a *folder* named `preferences.cfg`, not a file. Then ConfigFile can't load this path as it's a folder.
Removing those two lines might be enough to fix it (you don't need to create the `user://` directory, Godot does it for you).