Indigenous is used politically to describe people who have been subjected to colonialism and the nastiness that goes along with that, like forced assimilation campaigns and even genocide.

While technically yes all humans are native to Africa, no one's yet come up with a better term to describe groups such as Kurds, Assyrians, Armenians, Ainu, Chechens, Chukchi, Buryats, Cham, Sámi, Navajo, Cherokee, and Maya.