I don't think I would know whether it made a difference unless I tried it. It could be difficult to determine whether the sight glass is not moving sufficiently due to the restriction of the screw hole opening or the plastic itself. Very small movements in the sight glass make significant changes in accuracy of cut, as you already know.
Thanks Jeff! I filed the edges of the sight lens very slightly and re-performed the calibration process. It's now dead on the money (as is the fence angle (I had to modify the scale slightly by elongating the holes) and the pin distances to center of mortise. All in all (once you get used to the process) the tool is quite easy to align.
Thanks again for your help.
Dave