Not really. Although the genetic diversity across the entire continent is higher, limits to mate selection is common. Location, culture, economics, language, etc, all limit the genetic pool that people have to choose a mate from. So in-group inbreeding is relatively common.

Humans have lived in smaller groups with limited mate choice for most of our evolutionary history. A lower level of inbreeding improves fecundity (around 4th cousins). Once the inbreeding coefficient gets to around 2nd cousins, that’s when problems arise. This happens often in small tribes.

Smaller polygamous groups quickly develop issues with inbreeding. The entire group often has an inbreeding coefficient around 1st cousins or even siblings (example - polygamous Mormons).

Now Uganda is a bit different because the polygamous group is large. This limits inbreeding effects.