You seem to be forgetting that dogs were mostly selected NOT by nature, but by humans.
Selecting certain individuals to breed with is not the same process we see in flatfishes. Your post suggests that wolfs can become dogs within the time limits of a young earth creationist's view, but can a regular fish become a flat, a-symetric fish within this time (without the selective breeding we have applied to pets/domesticated animals)?
Is 6000 years enough time for a fish to change from a 'left-right' physiology to an 'up-down' physiology?
(I have no idea, to be honest. I haven't been able to find useful informatin on the web, but I think it is an interesting question to think about)