OK, and let's suppose the hole in the neck is perfectly in line with the body as the collet die is supposed to produce even with less than perfect brass. And furthermore suppose the bullet was seated right down the middle of that hole. Now when you place the round in the concentricity checker, with the support points on the case body, the bullet shows very little if any runout.

But also suppose the case necks are three thousanths thicker on one side. Does that not affect how the bullet is pointed down the throat? Thick side down, higher bullet. Thin side down, lower bullet and so on.