Much to ponder.
First of all, I think there is no single "perfect" anything. The strongest of any species must be adaptable, and that requires variations within the species so that, hopefully, at least one of those variations will be able to survive the unknown challenge thrown at it and the species will survive to multiply and further mutate. Varroa is constantly adapting and changing, and a stagnant "superbee" species will eventually be doomed.
As for things like tornadoes, bears, and the stupid neighbor with a can of "Raid," this is where nature needs quantity. Some of the strongest will, by probability, succumb to unpredictable threats like this. With luck, these random occurrances will not wipe out ALL the individuals with a certain beneficial trait.
Humans have been a detriment in this regard. Feral bees never congregate in such a manner that tremendous numbers could be decimated by a single tornado/bear/flood/wildfire/whatever. Bee yards and stacks of hives on trucks are not natural. Perhaps there is something to be learned here.
“The keeping of bees is like the direction of sunbeams.” -Henry David Thoreau