Sometimes I feel like including Africa was just part of the ruse, as we recognize it as a central location in the MG lore and very important to Big Boss creating Outer Heaven and putting everything in motion for the rest of the series. There's also like you say big stuff that happened with Gray Fox and Solidus Snake there in a similar time period. It's almost like Africa was implemented to get our hopes up about this actually connecting with MG1 and being the missing link only to be trolled by the ending and for it not to be all that relevant in the end.
As far as Venom Snake's story goes was Africa really essential for this game? I felt the opposite before release for obvious reasons, but actually experiencing this game's story myself it felt like the main setting was really Soviet occupied Afghanistan and Africa felt tacked on. Bulk of the missions are set in Afghan, the region we could explore was bigger and it's also where Sahelanthropus and XOF's headquarters were located. Final mission of Chapter 1 to get revenge on Skull Face brought us back there too. Quiet's final mission is also set there and she obviously got more attention than other areas of the story did. All you'd really need to do is relocate Code Talker and remove the child soldier subplot (who I thought were very disappointing in that they didn't do much with them, plus they cut Eli's ending anyway) and it would be kind of the same campaign I think just with even less variety in locale.
I mean, I know some people think the "real Outer Heaven" is referring to Zanzibar Land, but in the ending timeline if we're taking it verbatim it states that real Big Boss (not the phantom) created the Outer Heaven fortress in Africa while commanding Foxhound, but only states it's the phantom who perished there in the end. So I assume those events in Africa we were expecting to happen with Gray Fox and Naomi all actually happened behind the scenes where the story of the real Big Boss was occurring around the same time.
If my interpretation is correct and Venom didn't create the fortress from the original game, then I feel like Africa as a location really had little relevance to telling Venom's story and was tacked on to sell the idea that it was a straightforward Big Boss' closing the loop story as everyone expected.