On the overall balance I think the addition of the upper rack is a positive move. I did have one queen venture up through it on one hive late last season and she filled some drone cells and went back down.
So far, on 5 hives this season, no queen has ventured up.
I only added the upper racks in the last few weeks as it got hot here and immediately noticed a significant diminishment of bearding - ie: less stress, happier, healthier bees. Hard to see a negative there.
I wonder how one would define a "natural" honeybee colony these days; my thought is that any manipulation by man, no matter how benevolently intended, renders a colony un-natural. But it does sound cool, it has that going for it.