Hooray, a Devil's Advocate! Maybe you can help me out with questions I've wondered about. I have many more questions than answers.
Do the needs of the rodents equal the needs of breeder and baby snakes? Wild fox snakes have raided my father's pigeon cages for eggs. Wild corn snakes and bullsnakes like eggs, too. Do eggs have some benefit that rodent prey lacks?
Do the commercial rodent breeders let the rodents sit around for a few hours without food between selection for killing and killing/freezing? This could reduce any gut-loading effect from the pellets. And food pellets slowly oxidize and lose vitamin content. Do the rodent breeders always use the pellets before expiration date? These are questions I cannot answer but which could affect the snakes' nutrition.
Why do some breeders produce fewer bugeyed snakes than others? Sheer luck alone? Could a snake with a specific morph need a higher level of a specific nutrient to develop than a normal snake, and some breeders, by luck, do a better job of catering to that need?
Bugeyes are fairly common in homozygous lesser ball pythons and homozygous leucistic rat snakes. These are (probably) different genes in different snake families, but both produce blue eyed leucistics, some of which are bugeyed. Are these genes in the same biosynthetic pathway?
I think we are seeing a higher instance of defects in captive breeding compared to wild breeding. A higher percentage of slugs, vertebral kinks and small/missing eyes as well as bug eyes. This is across the board as well as in specific morphs.
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