what happens to the physical bodies?
While in the vessel, the body of the person entering the portal is temporarily in an unidentified location (another dimension?) for 15 minutes, until it reappears by the Jersey highway. The body is somehow transported from the 7 1/2 office to Jersey.
One could assume Craig's body was in this 'limbo' for 8 months, when he finally exits the Malkovich body, but what happens to the bodies of those who enter a vessel permanently - a) Craig, unwillingly trapped in Emily's mind, and b) Captain Morton when he entered Lester, and Lester and the older people when they enter Malkovich?
It would seem like they just 'disappear' from the 'real', physical world, vanish without a trace?