More crazy thoughts
The voice that tells Dolores to kill him at the end sounds like a modulated version of Bernard. So I think you are right in that Bernard might be linked to Arnold instead since the voices are Arnold. I am now also coming back to the thought that the MiB is a robot. Him and Bernard were Arnold's last creations before he was murdered as a fail safe to carry out his work. Bernard to further the consciousness of the robots and the Man in Black to solve the maze and set all the robots free. When the little girl says the maze isn't for the MiB I think it was built by Arnold as a physical backdoor to the system of Westworld.