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If I were to drill a hole, it would be in the brood box only, above the handle/hand hold. The main idea, as I see it, is to help minumize congestion in brood area, lessen the chance of backfill to minumize swarming and keep the supers' wax cleaner.
Honey stored in the brood area. This can happen if there is too much congestion and the bees start filling brood comb with nectar and pollen. This normally happens in the spring but anytime there are supplies entering quickly this can happen. This is what I've read and I expect what I've experienced since I have gone back to bottom entrance for some hives and upper for others, get my own idea and find what works best for me. Two bottom entrance swarmed and the other one was a swarm from this year. The top super was not drawn out, I may have caused that by adding it late this year, on both hives. They have since been drawn and filling up nicely.