The round pit--is that something like where Kira found the Seed?

Yeah, I think it's called The Beacon or something. You never actually see it in the book.

I assume it was made by the long-gone entities, which I want to call the Builders except I think that's from The Expanse?

The Vanished, who basically seem to be the equivalent of Paolini's elves/grey folk. We don't learn anything about them in the book other than that they made the Limp Dick and its fellows, as well as the pointless Staff of Blue.