When Diamond asks how Africa became black, he is asking how and why the Bantu peoples in Sub-Saharan Africa came to dominate and largely displace the Khoisan and Pygmy peoples. His argument in Chapter 19 about this mirrors his argument in the book as a whole. What he is saying is that the Bantu people were luckier in terms of where they arose. Because of their geographical luck, they had agriculture and technology and were able to displace the other ethnic groups which had none.
Basically, Diamond is saying that the Bantu's ancestral homeland was in a place where there were crops that could be domesticated. In addition, it was near enough to North Africa that it was able to get domesticable animals through diffusion from the Middle East. Because of these advantages, the Bantu were able to have larger and sedentary populations and could create and borrow technology. The Khoisan and pygmies, whose homelands did not have the advantages of the Bantu's homelands, were not able to have these things and they, therefore, got displaced. In this way, Africa "became black."