In Maxtrix 2 and 3, NEO is able to control and see machines as codes (the logged out world). But, did he really escapes from Matrix at all? It could be Maxtrix0.5, a back end server managing user accounts DB. The fact that even the agent AI can be transfered to this world means, it is also digitalized envirnment. IMO, NEO is still trapped inside Matrix, but, they just think they are not because of the terrible condition they are in. But, the reality is switching from fake human world to fake hell, he is still in a fake world.