tl;dr The people of that area in East Africa naturally live close to sea level, however there are easily accessible elevations changes that distance runners have trained on for probably centuries. It turns out that training at high altitudes and recovering at low altitudes provides a tangible and demonstrable advantage compared to just single elevation training.
India's Deccan Plateau is about as elevated as most of Kenya's highlands and takes up basically the entire land area of India that sticks out into the ocean
No idea about the other two, but India's sports administration is corrupt to the core. Funds are stolen by those on top, and athletes who complain - even about obviously criminal things like sexual assault - are pushed out. Some sports bodies (chess, for example) are better, but the big ones (cricket, wrestling, football) are mostly bad.
Yeah like the other commenter said this isn’t it, nobody is commuting up and down 10,000’ on a regular basis, especially in antiquity. Just because different elevations “look close” on a map means nothing.
Far more likely is this is a concentrated population of folks with highly desirable traits for distance running.