It is at least one method n swarming preventing. When one box is full of brood, queen start to lay empty combs under excluder,With double brood box you will have to check to make sure the queen has free access to top and bottom box. I have seen double broods with a QE in between the boxes. ;
Is it to not put a brood box on the floor if it may have the queen in it?It's nothing to do with handling the queen more to do with making sure she does not escape. Think about it.