Mixing is how genetic inheritance is supposed to occur, but that is not always the case as we see with Chimeras. There is no apparent rhyme or reason to how these genetic anomalies occur, like I said unlikely but not impossible.
I would assume there are some differences in genitalia as there are between many closely related species. Now the vet would need to have pretty vast experience with both, but it just doesn't add up to me why they would say that to suggest this otherwise. In all likelihood this came down to a miscommunication between a vet and the owner.