I'd be very interested to learn your background. I apologize for my inflammatory comment if my information was incorrect in any way, as I said I'm no geneticist that is simply my understanding.
I'll give you the fact that these alleles can exist in singular copies due to deleterious effects however I'm not sure I'd be willing to give you the rest of that. I'm not aware of any instances in which alleles exist in triplicate. Due to the structure of DNA it does not make sense to me how this would work. Can you cite your example? I'm genuinely interested in how that might work.
It seems odd that the inhertence patterns would be as such if the mutation was due to an alteration of multiple genes. What you're suggesting is that due to the close proximity of these genes on the chromosome they are always or almost always passed on together right? I suppose this is possible, if this is the case I'd be interested to see what would happen if recombinace occurred and one of these genes were lost. Would we then be able to isolate specific traits of the "genes" in ball pythons? I'm rather interested to hear what you think is going on here however this is really far away from the intended discussion. If I didn't offend you and you care to explain I'd love to hear a pm about it.