Hi Ken,
Basically the calibration of the Analyser / ZoneMaster is intended to cover only the linear portion of the paper curve for exactly the reason that the toe and shoulder areas are non-linear. The calibration of early models was based on a mid grey but this caused problems with the shadow/highlight areas with papers whose curves differed significantly from the standard Ilford MG IV. The late lamented Kentmere Art Classic and Kentona are examples of such a paper.
Setting the end points at 0.04 log.D for the highlights and 90% of Dmax for the shadows avoids the toe and shoulder areas of the paper curve where density is a non-linear function of exposure, and that's why we suggest using those densities for the grey scale endpoints during calibration. Some papers have less linearity in the "linear" portion of the curve than others, so you are correct that the mid grey can vary from paper to paper. For this reason the products feature a special 15-step "test strip" mode which allows you to make your own grey scale strip based on the calibration end points you've chosen; this will maximise the match between the meter's indications and the results on the print. In practice few people do this, but the facility is there for those who need it. If you routinely tone prints for example, you can make a toned grey scale strip to improve accuracy.
Our calibration procedure was designed to give good results across the range of available papers and to avoid potential difficulties in the toe and shoulder areas, but the meter's flexibility is such that you can choose your own end points to suit your own requirements.
Hope that helps!