Because the bees will bring in pesticides and other unwanted chemicals that the wax will soak up like a sponge, so every few years you will want to ratate the comb out so they produce fresh clean wax. The easiest way to do that, is to pull that bottom box in the early spring when the bees are in teh top box. Set the #2 box on the bottom board, with the #3 box on top of it. Put new comb in the old bottom box.. if your using foundationless, you simply cut the comb out and drop the frame back int eh box, and put it on top, making it your new top brood box..
In using mediums, I winter in three medium boxes, its the same volume as two deeps, so I rotate my comb out every three years. The added advantage is moving the bees down a bit so there is room above them as they rebuild that comb. Every so often they get stubborn, and decide NOT to move down.. so in effect, they feel crowded up there in that top box and decide to swarm, despite the fact that they have two empty boxes under them.
Another issue, is if they decide to fill frames with honey in that bottom box.. what do you do with it? You can extract them, or freeze them.. but they will need to draw the frames you replace them with... If you have all the same size box, you can move the honey up where it belongs, while moving DOWN a drawn frame to open the brood area back up... They dont have to draw it out, its already prepared.
There are quite a list of reasons to standardize your boxes/frames.
What you are doing will certainly work, I'm just trying to point out the advantages of having your frames all the same size. If he likes deeps, then go with all deeps, but make HIM lift them.
That will fix his wagon!!!
