And in case anyone is wondering - the other advantage of allowing free movement of bees between boxes is that in the initial manipulation when you put all the brood up top, you don't need to worry about whether there's enough bees to cover the brood.
All the nurse bees will naturally migrate to the top box to care for the brood, leaving an even emptier box at the bottom so more room to discourage swarming, as well as fewer nurse bees for the fliers (the swarm instigators) to try and coax to swarm