River systems matter.
Population genetics is influenced by various natural objects. Especially prior centralized kingdoms and roads.
High mountain ranges acts as important barriers. But how genetics is shaped when there are multiple ranges? Well judging by ancient DNA we see from historic Armenia it seems river systems ( or water basins ) were also important in shaping genetics prior centralized kingdoms emerged.
Historic Armenia has two important basins. One is the Kur-Araxian system which is part of Caspian sea basin. The other one is Tigris-Euphrates system part of Gulf basin. Then there are also two closed basins. Van basin and Urmia basin. I didn't add the Black sea basin because it's a small portion of historic Armenia.
I think the differences we see between samples from RoA and South Eastern parts of modern Turkey can be explained also by river systems and lack of large mobility between this basins in pre historic times.
But overall this differences are not higher than between historic Armenia and Anatolia or Iranian plateau.