That's an excellent find Bob!
Now I'm going to have to check out the other engine rooms. Another tell-tale sign is the button at the top of the barrels (or the cylinder caps). The smaller diameter barrel the button is indented in while the larger diameter barrel the button protrudes up.
So the smaller barrel faces the cathedral in "Is there in truth..." and it faces the opposite direction in "Elaan of Troyius". The dilithium assembly in both cases still faces the control panel wall.
Edit: "The Immunity Syndrome" with the backward facing engine room has the larger barrel facing away from the cathedral...