Wouldn't you have to prove it out to see if the "small eye" is genetic, just like any other trait? The problem is that it's not ethical or practical to prove out a line of deformed snakes just to see if it's genetic. So we may never know. But then again how did the head wobble on spiders propagate? Someone must have known and just kept breeding and selling them anyway.
If it is genetic or not, it does not change the fact that this person is claiming that he was sold a snake with a deformity, and was not told about it up front. That is wrong in my opinion.