I think I've got a basic setup that can cleanly handle loading in "rooms" that will make up the level. I almost overcomplicated it but then I just made it so that each room is a Godot scene and I just bloody preload them all at the start and then instancate them one by one when the player clears a room.

I can get away with this as it's just a simple twin stick shooter and not proper massive, complex levels.