In Darwinian evolution, the source of variation is irrelevant. Selection will, in the long run, determine the shape of species, even those that have been manipulated by humans.
Again, the demigod "Natural Selection" steps in. Fortunately this allpowerful figure seems to have little effect on the HOX genes eh?! Else we might have 3 eyes and 6 legs from time to time, and you can't say that system doesn't have some competitive advantages.