Yes, you're quite correct there Adrian. Of course the dilemma is that there are so many different string types, gauges, and setups that it is impossible to display a universal final pitch chart without being tailored to one particular setup. Based on this limitation (and admittedly a sense of futility), the pitch charts I show only demonstrate how the pitch would differ from standard 2^(1/12) spacing at any given fret, assuming all other string and setup factors were to remain constant.

So if the chart shows -2¢ at the first fret, this is not meant to indicate that the final pitch would be 2¢ flat there, but simply that it would be 2¢ flatter than it would were the frets and nuts placed standard. This inevitably introduces a bit of confusion to interpreting the charts, but unfortunately I had to conclude that it's the best I could portray them without having data about an individual instrument to be focused on. My spreadsheets are capable of accepting input data about actual pitches on real instruments and calculating changes from there based on various alterations, but for general use a relative pitch shift is the best I could do.