I have a lot of hives both ways. I don't think there is a lot of difference. I have several DE hives, several DE mod kits, several of my version of the DE mod kits, and lots of hives with various top entrances. I like the warm way. It's easier to work. The bees don't seem to care much, and I don't think it's worth a lot of effort to convert them, but if I'm building something and have the choice, I go the warm way. But if you let them they will build their combs in the box this way:http://incolor.inetnebr.com/bush/images/BroodNestInFeeder.JPG
This is neither. It's a bit of a comprimise.