You only have to seat wadcutters flush for the special semi-auto's made to shoot them in Bullseye matches, like the Smith & Wesson model 52. They won't fit in the magazine or feed properly if you don't. Revolvers don't care all that much how you do it.
It sounds to me like you are adjusting the whole die body just to change seating depth. The seating die should have a separate smaller threaded screw or knob on top to adjust the seating depth. That allows the crimp and bullet depth to be adjusted independently.
Tell us whose make of die you have and we can tell you how to set them up.
This Lee video is good for general purpose seating die adjustment. Pay particular attention to the fact he does not let the die body turn when he adjusts the smaller seating depth knob on top.