The company has changed the scanning/measuring process from what it was many months ago. It used to be that when the scan happened using proofgrade materials that the head would take a measurement in the center of the bed. It was independent of where the design was placed. If the measuring beam did not hit your material then the cut would be ruined because the focus was way off. They went through several iterations of where to take the measurement. Now it works pretty good.
The height measurement is taken at the same spot as the design and will hit the material if you have placed the design properly. I guess my point is, yes they take a height measurement for Proofgrade. It also does it for non-Proofgrade but not sure how the information is used.
edit: It doesn’t take the measurement in the middle of the design but it is at least part of the design. If for example you have a dozen tokens you would want to cut spread across the bed it would choose one and measure at or near one of the cut lines.