After reviewing the arguments, I actually agree with Smurph & B-Dub. The ship (Plex) was actually used as his base of operations in his mini series. He was a prisoner in The Cube before taking it over in Illuminatti #4, so it wasn't his actual base of operations as much as his place of confinement until he was set free by the Avengers.
So (Smurph/B-Dub) you'd have access to The Ship but not to The Cube.