Why would waiting for the patch change the setup of Africa? Keep in mind that even if there are no organized states, as in V1 the provinces do have POPs all set up and existing.
Yes Africa had people, but for the most part they lived under systems of governance that Paradox has decided does not fit in with the systems of government that exist, and that the best solution for modelling the colonization of Africa in this period is to model it based on areas that can be claimed by outsiders and turned into colonial segments of empires.
Note that not all may agree with this, including some within the modding community, and I feel exceedingly confident that the wide ability to mod Paradox games will result in mods that treat the state system in pre-colonial Africa differently. But I would not expect any changes via any sort of official patch, as there were no new African state (or any active states pre-1920) added by Paradox in any of the 4 patches or 1 expansion to Victoria 1.
From my understanding, which is not complete, as I only realave an interest in Southern African history, is that most Africans were goverened by their tribes, etc. Their formed groupings were generally quite small with very few having territory extending any significant distance. The Zulu's made one of the largest African Tribal kingdoms in Southern African history, and look how small that was. And even then the rule was quite splintered and very inneffective.
The reason it is represented however is that it was capable of rallying their armies to fight off external groups, and did have a system of local and "national" government. Something most all of the other African tribes could not do and did not have.
The choice not to represent some of these countries is appropriate in the areas were they had no significant national identity.