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Spherical aberration is quite hard to visualize, but imagine that you could separate the light passing through the lens like an onion, in several concentric layers. The middle would be very high F-no's, the outer layers would be the lowest F-no's (largest apertures).
Light comes from one POINT in the scene, passes through the DISC of the aperture, and is concentrated to a POINT on the sensor again (if the point in front of the lens is "in focus"). Spherical aberration means that light passing through the aperture closer to the rim is not focused at the same plane as light passing through the middle of the aperture.
Most lenses have a positive SA, meaning that you get "focus shift" as you stop down, the plane of best focus moves backwards as you increase F-no. This is also what gives "smooth bokeh".
Your camera MEASURES focus at roughly F/5.6, meaning that it measures the light passing through the lens at an ANGLE of F/5.6. Light passing through the lens closer to the middle of the aperture (F/11?) and further out towards the edge of the aperture (F/2.0?) is ignored, blocked out by the optics in the AF-module.
Now, if a lens has less SA, the focal distance difference between the F/5.6 "layer" and the F/2.0 "sum" of light will be smaller. And if the lens has more SA, the difference will be bigger.
The D700 is quite probably slightly back-focusing, a behavior that fits perfectly to most fast lenses, like the 50/1.4, 85/1.4 and 135/2. The back-focus perfectly offsets the amount of focus shift from F/5.6 to F/1.4-F/2. But since the 100F/2 macro has less SA, you get less focus-shift, ending up with a system total @F/2 of a slight back-focus.
And no, I don't think the AF-adjustment works if the camera doesn't receive a lens ID - which you don't get from the ZF-lenses before the ZF.2 update. But the "front on/off limit" dot trick should do the trick, if your sample picture is about the "average" error you get.
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