Strains, names and genetics are all a big mystery in Indonesia not because the industry is good at guarding trade secrets, but because there is no standardization in regards to Kratom (or anything else for that matter, really). I wouldn't even be sure that the gas I'm buying from there is really unleaded just because it had that label. Why would I say such a thing, when clearly such intricacies exist when it comes to other therapeutic herbs like Cannabis? A review of the scientific literature would indicate that there are 3 strains, not just 2. Currently, the known strains are Rifat from Thailand, and Bumblebee from Vietnam. It is very possible that there could be more, as the plant grows with relative ease throughout Southeast Asia. However, genetics have not been mapped or documented well enough to arrive at that conclusion.
The process of Natural Selection could have, over hundreds and thousands of years, created genetic mutations that were propagated through natural breeding, or passed between regions through cloning. Seeds are illegal to sell in Indonesia, so primitive breeding techniques at best, have been incorporated. The idea that nature has done a better job than farmers is more realistic than the idea that all of these "strains" were genetically crafted through breeding.