I live in a very similar place (Bahia in Brazil, which has a mostly African derived culture), and we have the same bananas here. I assure you that they are not the primary calorie source, although they may be a prominent part of the diet. In any case to get those GM bananas into the hands of the people who currently eat the non-GM bananas you're going to have to organize a huge logistical operation of producing millions of GM banana offshoots (remember that bananas have no seeds, they are all clones) and distributing them to millions of subsistence farmers. Possibly doable, but definitely more difficult than distributing papaya seeds (one papaya has hundreds of seeds and they store and sprout very easily!) And they can grow some papayas alongside their bananas... like I said they like the same soil conditions and they actually grow well together.
Also in the case of Uganda by far the easiest solution is make sure there is unprocessed red palm oil available on the local markets and that the people know that it's better for them than the processed oil... it is a superior source beta carotene as well as Vitamin E and some other essential nutrients, and Uganda is a major palm oil producer. Probably today almost all the palm oil produced commercially in Uganda gets processed and exported, which is the real irony in all of this... they probably destroy enough beta carotene in the processing of commercial palm oil to cure Vitamin A deficiency in the whole world!
(To explain the above... the oil plam produces two oils, red oil from the mesocarp and white oil from the kernel. The red oil, unprocessed, is very rich in beta carotene ((which gives the red color)) but has a strong flavor that makes it unsuitable for industrial food use. So they process it to remove the color, smell, and flavor, then the ship it around the world to use in junk food and other delights of civilization.)