If 2 and 3 were even partially destroyed, why haven't we come across breaks in the walls, like we have in The Core? Unless you're referring to how the basement of Layer 2 seems more aged.It is possible that the outer rim spread to other layers, likely including #2 (super advanced computer that was integrated into the defense systems) and #3 (at some point visited and damaged by Mur.) A couple of years after the creation of the Root, Mur discovered his karma arm, and began experimenting with it. However, his portals caused massive dimensional stability, eventually reducing most of layer 1 to a black void.
About most of Layer one being a "black void" - Besides the Edge, there really isn't evidence of this. However, from the secret note in Sub8 about what Mur's destroying, maybe Layer 1 is the "flawed copy" and destroying Layer 1 is his endgame.