I hate to post this video as it is somewhat graphic but it really addresses your concerns. I believe this animal is a chocolate butter ghost. None of those genes are known to have defects as far as I know however there is clearly something very wrong with this animal.
https://www.youtube.com/shared?ci=BZJo_2sM9hQ
If there's a 1% chance of hatching a ball python regardless of the genes at play should we avoid breeding them? I understand this is your argument taken to a ridiculous extreme but the point is there is always a chance of defects regardless of the genes at play.
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