Truthfully how many super ball clutches have you seen? Here is one that could be easily confused for a ball by someone with little experience
I have seen some T. radix hybrids that look exactly like their parent, and isn't this the thing the entire anti hybrid crowd base their hysteria off of? In a polyploid situation you end up with the genetic information translated my mieosis from that specific pair is an exact copy of the parents dna. If the chromosome that codes for exterior looks is ball and the chromosome that codes for internal organs is blood then you end up with the situation the vet described. We are talking about a very specific combination that would likely not pop up often, and in general you would end up with animals that is a mix of the species.
I hear you and I admit that I don't know much about snake genitalia. It seems pretty hard to find pictures of blood python hemipenes. I think it would more strange if they were identical based off my experience with biology.