I am using top entrances and, in the case of my biggest hive (7 mediums at the moment) both a top and bottom entrance.
Most of the brood that has appeared in the honey supers has been drone with one exception in the big hive; in that hive box #5, the first super above the upper slatted rack, was largely filled with worker brood - a perfectly filled frame. Also, that's where the queen was on that particular day. After harvesting I re-configured that hive with all of the brood back below the supers. All 4 lower boxes were solidly full of brood and honey, so much so that I moved some frames over to my other 2nd year hive and replaced with undrawn foundation.
My thoughts: Admittedly, 14 months or so with this setup is not a huge period of time to come to definitive conclusions but.... so far I couldn't be more pleased and feel that it has vindicated itself many times over. The queens seem quite capable of moving up through the upper slatted racks at their whim, a habit that seems to be encouraged by using top entrances. At the same time, their ability to lay anywhere is, as you noted, easily remedied due to the universal nature of the all-medium setup. The ability to move frames anywhere in any hive is a powerful management advantage. As for honey production, with even a moderate flow this fall I could hit 300 lbs easily in the big hive (maybe 450 lbs total for the 2 second year hives combined) and even my 2 nucs have grown quickly and have unusually large amounts of honey. All in all 4 of my 5 hives are doing far better than I expected this year and the 5th, my problem hive from last year, is catching up.
Only one mild disappointment - a bit more varoa than I had hoped to see. That's in contrast to virtually none last year. I'm wondering if last summer's intense heat could have been a benefit there - we have yet to experience any real prolonged hot weather here this year.