> Inbreeding is a tool.  Inbreeding allows the breeder (or "nature" in my example) to fix traits within a population.

Inbreeding may be a tool in the hands of people, but nature doesn't use tools. In evolution, things usually happen as a net result, not by the use of tools or strategies, etc. What humans have achieved through breeding stands separate from what occurs in nature as a result of natural selection. 

Natural selection has no goal, such as better bees. It is the net result of millions of different species battling to survive. Out of this battle, certain survival strategies develop, such as honey hoarding in the case of European bees, absconding in the case of African bees, migrating in the case of bees in India. Certainly luck plays strongly in this game, some get lucky. 

Another example of natural selection producing a solution to a problem is the breeding system of honey bees. They seem to make a concerted effort to avoid entirely anything that could cause inbreeding. The queen and drones fly far from home and she mates with as many drones as possible, 50 or more in some species of honey bee. 

So the idea of bringing queens from 50 or more sources into a breeding program would seem far more natural than to arbitrarily select a few queens based on a superficial evaluation of "desirable features." If we have learned anything from breeding plants and animals, is that it is a mistake to focus too hard on too few traits. Examples of freaks abound, from roses that look great and stay fresh but have no scent to livestock that cannot survive without antibiotics.

So you say, breed for hygienic behavior, and to heck with other qualities such as color, honey production, temperament, etc. How do we know if hygienic behavior is the most valuable trait in survivability? Maybe the most valuable thing is to avoid breeding strategies of any sort. Or to copy nature, and try to get as varied a mix as possible, at least in the case of bees.

For example, how does nature produce new colonies? Charlie Mraz mimicked nature's way when he made divides. He would select the hives that were doing the best in spring (ones that probably would have swarmed anyway) and divided them in half. The half with the old queen becomes a new colony, same as in nature, and the remaining half must develop a new queen from eggs she left behind. That queen mates with completely unrelated drones and produces a colony which may or may not resemble the parent in significant ways. It may be that almost none of the traits of the parent are passed on to the offspring.

There are people working on this idea of intercolony diversity and the synergistic effect it has on colony personality. But the fruits of their labors are in the years to come. It wouldn't surprise me if everything we think we know about the breeding of bees turns out to be completely wrong. 

Finally (finally!) it may be that a colony, when it divides to form a new colony, passes epigenetic characteristics to its offspring. These could be environmentally switched on alleles, acquired behavioral traits, or microbial complexes developed in response to specific pressures on the colony which enabled that particular colony to prosper where others did not. 
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