As long as there is bee space between the boxes, the bees don't care. I have run 11 frames over/under 10 for a couple years now and the bees do fine.
I plan to fix that when I get a new queen laying, as I want to do a summer split and overwinter a nuc this year, and will put narrow frames in place of the standard ones in the brood nest deep. Both mediums (one under, one over) are 11 frame narrows, works great.
So far I've found that narrow frames work very will in the brood nest. Comb is quite flat and there are very few drone cells (this may be because I have two foundation less frames in there that are solid drone cell). They do not build the honey arch over the brood wider than the brood cells, and I think it's easier for them to keep the brood warm in the winter and early spring -- certainly this hive produced a huge population very early, and had a shallow and a medium FULL of bees in early March. Had to feed them, but I don't mind.
Peter