If further evidence of my pedant qualities was required, I should point out that most taxonomists would agree that there is no genetic difference between what is called the greater kudu and the Cape kudu. Both are Tragelaphus strepsiceros. Some people suggest that there are in fact southern, eastern and northern greater kudus, as subspecies of the greater kudu, but most scientists I believe dismiss those classifications. I have not seen very many - in fact can't find any at the moment - who argue that the cape kudu should be recognized as a subspecies. Note that the IUCN does not recognize any of the purported subspecies, which you would expect they would, given their mandate.
As someone who has shot what would be called the southern greater kudu as well as the cape kudu, I can attest to the fact that the latter tends to be smaller than the former, both in terms of body size and horn size. Having said that, regional variations in color or size do not necessarily imply different subspecies. There could be many reasons why kudu do not get as large in the southern parts of South Africa as they do elsewhere, none of which are necessarily related to genetic makeup.
I think the southern greater and the cape kudus are distinctions made by hunters or more particularly outfitters, who can't charge as much for a smaller version of the kudu (unless of course it's a lesser kudu!), but would still like hunters to take both. In this connection I note that SCI counts the Abysinnian, East African, Eastern Cape, Southern greater and Western greater among the kudu varieties for which they permit record book entries. No scientist that I'm aware of agrees with those designations, but it gives hunters something to shoot for. (pun entirely intended.)