Both! By using the mean value or the difference between pairs of measurements you can adjust for different things.
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Joe,
Sorry about the previous short previous reply, I was away in Perth with limited time.
I assumed the long, fixed rails (X axis for me) were straight and then made them planar with the aid of a precision spirit level. The 65mm square rails they sit on can be shimmed at each end for this.
Using the wires gave me a reference plane based on the rails themselves without the step of skimming the base and using that with all the slight imperfections and ridges etc. that would produce.
As I described in the method, by taking either the difference or the mean value of the readings from two wires, one each in front of and behind the gantry (with the probe arm aligned parallel to the X axis), I got data relating to the tilt of the gantry in two directions which were corrected by shimming either both ends of the ganrtry, front or back (to correct what you have aptly termed 'nod'), or just one end, front and back for what I've called 'tilt'. I also got data about the twist (variation of nod) of the gantry along it's length. This was corrected with shims under the rails.
Once the above was sorted, the final measurement was made along a single wire with the probe aligned along the Y axis. This indicated the tilt of the spindle due to rotation of it's mounting on the back-plate.
These measurements were able to separately show the tilt of the gantry itself and the tilt of the spindle axis due to rotation of it's mounting which I think was the jist of your question.
I hope this clears things up.