Thanks Jimmy,
Your input was helpful. I emailed Chris when I didn't get much response here, and he was nice enough to send me the following reply. I think is a good explanation of the factors that need to be considered when calculating neck angles so I'll post it for all to see.
"The term may be a bit confusing, this deals with the height of the saddle above the bridge ( the optimal string contact point of the saddle above the surface of the guitar top). When you set the neck angle in the beginning, you are projecting the neck top surface minus the finger board to where the saddle will be located on the guitar top. Lets call this the zero plane or the straight line from the top of the neck projected to the guitar top. This is then the reference plane where you can calculated the height of the saddle, keeping in mind to subtract the frets and finger board from the bridge height and allowing about 3/32" saddle height, this is what I call height compensation. However there are other factors to consider such as neck relief, string height for playability, saddle break angle and string tension deflection. They may be small but are enough to effect he height of the saddle. There should be some adjustability to consider in the saddle height due to temperature and humidity, so it's best to calculate the average height so that you have some room for adjustment without effecting the performance."
I had an idea that this is what was being referred to, but it is nice to have confirmation.
Again a big thanks and recommendation for Chris and his Jigs at luthiertool.com
Josh
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