Dan -
It's a long argument with no right answer. I live near the Uganda - South Sudan border, so I'm less than 500 miles from some of the most advanced oil refineries in East Africa. Getting even 95 octane (R M average) is not a problem. Even jet fuel (Avgas with E2000 ratings) is easy to get. But in other areas it's harder. I would say premium fuel is easy to obtain in northern Uganda, South Sudan, much of Sudan, much of Ethiopia, and anywhere near Mombasa or Nairobi in Kenya. That said, if I'm going to an area I've not visited before, I will be more cautious and carry jerrycans. I also am careful to only patronise Total or Shell fuel dealers that have higher standards for fuel.
Diesel has some clear advantages, but I feel the fuel quality is not regulated nearly as well. When I drive our Hilux D4D, I often wonder exactly how bad fuel it will put up with - and never want to be the one to test this. Overall, the 3.0TD in our Prados is the most reliable engine in the group, but I've never gotten stuck (touch wood) with bad fuel or an engine problem. I love the supercharged 4.0 and I'm willing to put up with a bit of a fuel search now and then. But if I were "adventuring" into a region that I didn't know well, I'd probably choose a Prado TX 3.0TD.
Choosing layout of how you're going to store stuff and matching your suspension setup to the road conditions will have a FAR higher impact on your day-to-day quality of life in the field than which engine you have. Engine is rarely the limitation, in my experience, in East Africa. Even in eastern Somaliland we were able to get Shell petrol, albeit not from a formal station...