My interpretation of the movie is that Cobb never left limbo. The entire movie takes place in his dream reality. Therefore none of it--even the rules about extraction, or the fact that criminals do this--is reliable information. It's all explained either by Cobb or by Cobb's avatars. With Saito echoing dialogue from Cobb's memories with Mal, I don't see any other way it could work. But that means I have no reason to trust that Mal exists, either.

To me, it's kind of like Usual Suspects--at the end of that movie, the only thing you know happened is the opening scene. In this movie, all of it happened in Cobb's mind, and his perception of what is real is clearly faulty.

The fanfic assumes the top layer was real, otherwise there's nothing to build with. But I just don't see how that could work.