All the points you raise are legitimate and apply to all methods designed to fine tune the auto-focus.
1) Concerning the focusing distance, it is best to choose one for which the depth-of-field is narrow. First, it is only in such a setup that ultra precise focusing is really needed. Second, if the depth-of-field is not small, it is difficult to visually gauge if the focusing was done at exactly the right place.
For longer lenses like your 80-400 with shooting parameters, 400mm, f5.6, distance of 6m to subject, the depth of field is around 8cm (4cm in front, 4cm behind). I therefore suspect that even at 6m, a single test chart will be very efficient in determining proper focusing.
2) For zooms, it is indeed the case that at different focal distances, a different ideal correction might be needed. Hopefully, it is possible to find an average correction that is acceptable for all focal lengths. Otherwise, a Nikon repair center should be contacted.
In any case, whatever correction is applied, the final test (without any sort of chart) comes from trying out the correction on your usual subjects at normal working distances. If the vast majority of pictures turn out good, then the fine tuning is done properly for you.
All the fine focusing methods should be considered as aids to achieve good focusing but they do not replace real field testing.