Hello Ross,
Thank you for providing the sample project.
In Metashape Pro (and PhotoScan Pro) versions prior to 1.5.4 estimated control point coordinates displayed in the Reference pane (and the error values as well) were calculated based on minimization of the reprojection error only, without taking into account measured control point coordinates in space. So they did not correspond to adjusted coordinates from the bundle adjustment step, and were recalculated from weighted image measurements alone.
Starting from Metashape Pro version 1.5.4 estimated control point coordinates correspond to the adjusted values, that is, they are calculated taking into account both reprojection error and measured object space coordinates. Similar behavior is common for other software packages and also allows for better detection of the measurement errors.
If you are interested in the difference between measured and triangulated control point coordinates, you can temporary uncheck the corresponding entry in the reference pane (thus making it a check point). Please note that check point error calculation is not affected by the change mentioned above. Upon unchecking the control points you do not have to click on Update button.