But yes, it appears it is it.

With a booking from every other East African city, it is possible to get award seats on the flight I want.

With a booking from Nairobi, it is "unavailable".

Pretty darn sucky indeed. Looks like my commercial relationship with EK needs to end soon.

ETA: Confirmed by EK itself:

"On some flights, availability is determined by the ‘point of sale’ or country of origin. In which some seats are allocated only for passengers originating from a certain airport.
...
Currently, all seats allocated for reward flights in Economy Class are fully booked on EK flight 36 (DXBBHX) travelling from Nairobi and Luanda on xxx.

Skywards Flex Economy Class seats are available for the same flights if the booking is made via Addis Ababa, Entebbe, and Dubai."

So if looking to change B-C on a reward booking A-B-C, it is not enough for there to be availability B-C.