Not quite.

Tape the protractor on and have it's center in line with the output shaft, not the arm. Connect everything including the control rod and turn it on. Get the servo arm as close to center as possible but do not worry about where the surface is at this time.

Now move the surface using the radio in both direction and see if the servo arm is moving the exact same number of degrees. Adjust the control horn height and control rod length until it does, again, not worrying about whether the surface is centered or not.

Once you have it moving the same amount of degree's in both directions, then your mechanical geometry is perfect.

Now program the servo to center the surface. Once you have that move the protractor so that it's center now matches up with the servo arm and then adjust your endpoints so that you get the exact same amount of throw on the surface in both directions. Once you have this, then you should also still be getting the same amount of degrees on the arm in both directions.

When you are all done, the servo arm most likely will not be exactly perpendicular to the servo case but you will be getting the exact same amount of throw and most important of all the servo takes exactly the same amount of time to get that throw in either direction.

If the servo only move 35 degrees in one direct to get the surface to 45 degrees but moves 40 degrees in the other direction to get the surface to the same 45 degrees the speed will be slower when the arm is moving 40 degrees versus 35 degrees and if you are working on the ailerons then your rolls will not be axial and on the elevators, the faster side will cause the plane to roll to that side