I have not used those preset mortice height stop scales on my Domino, but frequently use the manual adjustment scale on the fence. I find I can get very close to center of the thickness of the stock using either of the following two approaches:
1) Measure the actual thickness of the workpieces with a metric caliper, then adjust fence of the Domino to one-half of the measuring thickness. For example, for 18 mm plywood, set the fence at 9 mm and of course, register the Domino fence off the top surface of the workpiece when cutting the mortices.
2) Mark the center of the thickness of the workpiece and then eyeball the center of the registration pins of the Domino with your mark. When using plywood it is pretty easy to see from the pin registration where the centerline (in the thickness direction) of the mortice will be located. I use this approach as a secondary check against any measurement/manual height setting on the Domino fence scale.
I recently had a need to join several pieces of 3/4 oak plywood to edging strips, some of which were 1 inch in width and others of which were 1 1/4 inches wide. For some of the plywood panels, the edging had to be flush with one surface of the plywood and for others, I needed 1/4 overhang of the 1 1/4 inch edging relative to both faces of the plywood. I used the above techniques to achieve the result I wanted.
Dave R.