The pupilary exit factor you describe is important with any none symetrical lenses. These are lenses where the aperture does not look the same size when viewed from the front and then from the back of the lens.
The macro D lenses are not symetrical so the P factor is important. The 50mmf1.8 lenses (which gives very good results with tubes or bellows)is about the only symetrical lens in the Nikon AF line up.
When setting the aperture USING A COMMAND DIAL on a macro D lens the body makes further adjustments to the aperture.
To keep it simple the exposure time at 1:1 is exactly the same as the exposure time at infinity.
In theory there should be a 2 stop difference.
The 2 stop difference is a acheived in 2 stages.
First there is the pupilary exit factor. At 1:1 it is about 0.15 stops with the 60mm D. about 1 stop with the 105 D, and about 0.66 stops with the 200mm D.
The remainder of the 2 stops difference is made up by physicaly opening up the lens aperture (by at least one aperture stop) to acheive a total of 2 stops.
You can see the aperture being opened up on a 105 and 200 D on a command dial body.
Set the aperture 1 stop down from full aperture. When you press the depth of field preview the aperture stops down at infinity focus and does not stop down at 1:1. The only exception is that when you select maximum aperture (unusual in close up) the aperture cannot be opened up and exposure time is increased.
The P factor for the macro D lenses gives a shorter effective focal length, a faster effective aperture (which makes the viewfinder brighter), and less depth of field than in a close up depth of field table. The "aperture opening up" part of the operation also gives a brighter viewfinder if you use DOF preview. The depth of field you see using DOF preview is half what you get when you set aperture using an aperture ring.
A bonus when using a manual flash or hand held meter is that there is no extension factor to calculate. All you have to bear in mind is that you have to stop down more than when setting via the aperture ring to get similar dof.
Photography is a bit like archery. A technically better camera, lens or arrow may not hit the target as often as it could if the photographer or archer does not practice enough.