SCOTT
All right, Mr. Spock, I'm now opening the access panel to the magnetic flow valve itself. Keep your eye on the dial. If there's a jump in magnetic flow you must jettison me and the entire matter-antimatter nacelle immediately. It will blow in two seconds after the rupture of the magnetic field.
I am beginning to think that maybe the "nacelles," include the secondary hull in this sense. One engine pod is the "anti-matter nacelle," one is the "matter nacelle," and the secondary hull is the "matter-anti-matter nacelle." Then all those various version from dialogue would make sense.

If you think about it, there is no reason for intraship beaming to be dangerous, if beaming over to a space station or down to a planet is routine. All beaming requires pinpoint accuracy, or else your feet might be melded into the ground when you arrive.
b) it only being dangerous to beam intraship when the ship is careening out of control at unsafe velocities.
Perhaps transporters are farsighted. To beam within the ship you need to use the special "reading glasses" mode. More seriously, it occurs to me that the transporter emitters are aimed away from the hull (one would assume), so they would have to beam backwards through themselves to materialize someone not on the pad inside the ship.
I'm going with the idea that intra-ship beaming is hard when the ship is at warp. They even have trouble beaming at warp from ship-to-ship early in TNG, because of the precision needed. So maybe the same thing applies when beaming within ones own ship at warp?