My guess is it was all intended to be part of the ship in the end, it just didn't start out that way. Different ideas threw things out of proportion, stuff like that still happens in films even today (remember the APC from ALIENS). But since the Derelict was the only thing visible, and you never really get a true scale of the thing, they expect you to go with the obvious. A chamber which does curve like the "U" of the ship, and has the same design throughout, situated directly beneath where Kane descended from.