I think that the site is even more mysterious than your post indicates. It appears that the hill under which these monuments are found is not natural. In other words, the historical site was deliberately buried at some remote time in the past! (perhaps for us to discover now).
Also, it seems that the genetic precursors of our modern wheat from all around the world can be traced back to wild grasses found within a few kilometers of the site! Perhaps this is the location where hunter gatherers became farmers for the first time?
A very mysterious place indeed!
I believe that The high amounts of sediments excavated now are caused after it was abandoned 9000 years ago. The reason why I belive this is because the structures are supposed to be 2 floors below ground making it sucessaptable to high sedimentation of dust and sand over time due to weathering of rocks and rain water rushing in from higher altitudes . I might be wrong but that is possible too. Nevertheless our theories conclude the same that they abandoned it later on. Perhaps the answer to the places lies in the trail they created after abandoning this place.
Also yes i agree that this was the place where homo erectus first started cultivating. After several thousand years.
I wish i could write everything I learnt about this place in one post. I probably can write a book on it. It's just mind boggling!
Also what do you mean by the hill is not a natural formation ?