When fired, a rimless bottleneck cartridge case touches the chamber somewhere around its shoulder. Its pressed there with 20 to 30 pounds of force from the firing pin spring. The case body may be off center against the chamber at its pressure ring depending on the bolt head mechanics. Sometimes, the case body doesn't touch the chamber at all when the primer fires.
Therefore, I believe commercial bullet runout gauges don't position cartridges relative to the dial indicator the same as they are relative to the bore center when fired.
A perfectly straight 3 inch long cartridge with its shoulder 2 inches from its head will have its bullet tip .001" off center in the bore if its head is .002" off center from the chamber axis. If all such cartridges are positioned that way, they're the same for all shots fired.