If you want to leave them on for the winter and you usually use an excluder, put the supers on top of the inner cover and the excluder on top of the supers and the lid on top of that. But I'd pull the supers after the cold hits. You can talk all you want about how the bees don't heat the hive, but stand in a small building/tent/shelter and then stand in a large one on the same day and there is a lot of difference in how warm you feel. Not becaue there is much difference in the temperature but there is a lot of difference in the radiant heat bouncing off of the walls.
I prefer the minimum room.
Yes the excluder is a problem. The bees sometimes move up and the queen can't and they lose the queen.