Your point is well taken...but a bit inconsistent.
The most attractive swarm trap (about the volume of a single deep if I remember correctly), is nearly useless for honey production.
Knowing what the bees choose for a nest is helpful when designing a swarm trap, but nearly irrelevant when actually managing bees for production.
I've certainly used and talked about using screened bottoms and top entrances...but I'm far from convinced that this is "better" or even "helpful". Our best overwintering colonies seem to have open screen bottoms all winter...but we have also had good luck with other configurations as well.
Natural nests have no frames, no airflow around the outside of the combs, no combs are ever moved or culled...no cells are ever exposed to the outside air and UV from the sun, no queen is ever pinched or "introduced", never split, never had queen cells harvested, etc.
I was once asked (I think on a TBH or Warre forum) if we buy treatment free honey from TBH's or Warre hives....my answer was that we had never been offered treatment free honey from such systems, but would certainly buy it (even by the pail if barrels were not available). I have a pretty good idea of what bulk honey sells for, and we pay top $$$...yet, still, no one has ever even tried to sell us honey from anything other than a Langstroth hive (and we get samples sent to us from far and wide). I think that such "more natural" configurations are fine, but I don't know of anyone making a living from them.