I haven't actually measured my boxes for a while. You must get drone comb between the boxes because you don't use an excluder. There is a bit of space above the bottom frames as well as below the top frames. I had the opposite problem, and on one inspection found a heap of bees squashed onto the excluder. So I think that if you use an excluder you need that bit of extra space on the top box because you lose that amount above the bottom frames. So of course I panicked and went and added a little strip to all my supers. It will depend on the size of the frames as well - they probably vary in height a bit. Anyhow, that bit of extra room might have been a bit much because there is sometimes a little bit of honeycomb below the frames, but I have to live with that now. I can't think of a way to evenly plane the boxes anyway, and the thought of transferring all those bees into spare supers makes me feel very tired!
I also have to live with our first 6 hives having 2 inches extra on the brood super, to fit the small hive beetle traps in. There are a variety of traps now, but when I found my first hive beetle I had to get hold of the first ones I could find. They do the job, but there is a lot of drone comb beneath those frames. I guess my hives are well ventilated for the tropics.