edit - just tested it. As the manual mentions, the dof preview button needs to be pushed in when making an exposure in AE. Verified this by taking a meter reading wide open with my 55 1.2 non AI lens - 1.2 @ 1/1000. Turned the aperture to f16 - with the dof button pushed in the shutter speed read as 1/8 sec. No film in camera, I took a test shot at f16 w/o pushing in the dof button, and the sound of the shutter clearly was much much faster than 1/8. I'm guessing it was 1/1000! Took another test shot same scenario but dof pushed in, the speed sounded much slower with a pause - just like you would imagine it to sound at 1/8 sec..
So, while the camera does automatically stop down the lens, the shutter speed is read at the wide open setting before the lens is stopped down. Which is why this does not need to be done when shooting in manual mode as you have already picked the correct shutter speed.