Another response by Etienne Patin, lead author of Inferring the Demographic History of African Farmers and Pygmy Hunter-Gatherers Using a Multilocus Resequencing Data Set, to a follow up post:
As to your hypothesis represented by the cladogram, this is a quite reasonable and interesting idea. Actually, the only method that we could use to prove it is to find human remains of Pygmies dating back to Bantu expansions, in regions that were colonized by Bantus. Population genetics cannot infer the presence of extinct populations. However, as stated in our article, Western and Eastern Pygmies may have suffered non-negligible population size shrinkages, which could be due either to Bantu expansions, or to many other factors such as epidemics. Another point in favor of your hypothesis is that some populations of Pygmies (not yet studied ethnologically) may live between present-day Western and Eastern Pygmy groups. Bantu myths often refer to a primordial population of small humans who guided them into the forests ("Pygmies were our compass", Kairn Klieman). Interestingly, Bantu communities living far from present-day locations of Pygmies know these myths (but this can be due to Bantu spatial migrations). As to the short stature, of course, a detailed analysis of the haplotypic context of these mutations will be carried! Thanks for your stimulating ideas!
Alas, it seems that human remains are going to be unlikely due to the climate of the region. Nevertheless, I would add that as the density of knowledge increases about the manner in which human populations arrange themselves, and the distribution of diversities of demographic histories, we can perhaps modulate our expectation about the plausibility of two alternative hypotheses whose likelihood can not be directly ascertained. In other words, some demographic scenarios may turn out to be far more common than others. Thanks to Etienne Patin for responding and elaborating.