Are those experiencing problems measuring to the Meplat or to the Ogive?
If the former, you will get variations, significant ones.
If there's variation measuring to the Ogive then it might be the seater plug being the wrong shape for the bullet shape whereby instead of coming into contact with the bullet on the sides of the tip, it presses on the tip. You can grind the seating plug in a little using a small drill bit if you're careful, which should ensure that the seating plug only grips the sides. Neck tension variations shouldn't result in much, if any variations as the seater is firmly placing the bullet to a fixed point. My money's on the Meplat's touching the seater plug base causing most of these variations.