It doesn't have to be perfectly centered in the workpiece, especially if your working with sheet goods. I thought it had to be centered as well when I first got my Domino, but I quickly learned to work with the settings instead of against them. For typical 3/4" (18mm) plywood, I use the 19mm depth stop setting. Using the depth stops allows your work to be repeatable and accurate, where sighting the depth scale will not. Just pay attention to the reference faces of your work, and don't worry about centering the tenon exactly.
Joe