T'Zeran mentions that astral ships do not generally have masts, as they function by willpower rather than through use of any sort of wind. He believes the ship will be fully enclosed, with two hatches: one for crew, and one for cargo. The dock is built to accomodate the ship, and if the ship lines up to collect cargo throgh the tube, it's passenger hatch should open near the door through which the party entered the dock.
The windows on the dock are larger than the portholes on the ship, but both sides should be able to see each other through those openings as the astral ship moves into position to dock. The windows or portholes could be blocked, but such an act would shout of hostile intent.