Do you mean the plastic stop on the lower rail to remember lower rail setting position? You can remove the plastic stop on the rail, you only need it if you change LRS positions several times or take off the vertical rail. You can fix the Nadir adapter without this stop in front to rotator side.
Did I understand you right?
Using RD3-L you have to strip the lower rail: take off upper and lower part of standard rotator and tke off detend ring and the yellow center screw. Then fix the black plate of the mounting set with the outstanding pins to the anti twist holes on top of the new rotator. Use the screw coming with the set 3/8"-6mm to fix the lower rail from top, then add the logo screw to top of screw. This indeed has a smaller diameter than the original standard rotator.