I don't think partially-filled or even empty boxes on the bottom hurt anything, since heat rises. If anything, an extra box keeps the cluster high-and-dry, away from the drafty entrance, and is prepositioned for spring.
Right now it looks like my two Warres will be overwintering in three and four boxes, respectively. They've drawn comb in all of those, and I figure they can store and care for it at least as well as I can. If they make enough honey on the fall flow I'd like to harvest a box or two, but right now they're both pretty light.