Unfortunately, as you've found, Nikon's in-body autofocus adjustment doesn't allow for different values at different focal lengths, apertures, or focus distances. Your suspicion is correct that those parameters can all change the adjustment required for perfect focus.
A common example is a phenomenon called focus shift: lenses with fast maximum apertures can experience changes in the plane of focus when stopping down from the widest apertures. Since the camera always focuses with the lens wide open and then stops down to take the picture (if set to a narrower aperture), lenses that exhibit this flaw may focus perfectly wide open but appear to need a slight adjustment when stopped down.
For in-body adjustments there's no ideal solution, but by calibrating the lens for the focal length and distance you'll be using most commonly, you can obtain an accurate calibration for those shots and hopefully be not too far off for the rest. It's worth mentioning that some third-party lens makers, notably Sigma and Tamron, sell docks that can be used to configure and calibrate their lenses, and those do allow independent adjustments at several different focus distances.
