Yeah, I mean beside the door I'll probably have windows showing a control room or something else important once it's finally detailed.Rather than making the door a passage for player. Make it a the doors to a more important control room (or whatever stuff is important in the map). This way you can keep it out of the playing area while still giving it a little bit of sense. The door in that case can be just a detail while at the same time making the system easier to understand.
I might go with this for the time being just so I can get a new version out.