Biggest cause of runout is excessive brass movement. Period.
I can measure my brass at ANY stage throughout the loading sequence and have less than .001" runout. I do not move my brass in ANY direction more than .003" total.
If you use .004" neck interference or more, you better have a really good seating system because all brass has a side that yields easier, even on turned brass, it's the way it's drawn. This causes runout.
Let me say this, I no longer measure for runout, it's irrelevant on groups anyway. The throat of your chamber WILL straighten things even though plenty say it doesn't. I shot groups with my normal loads and another group with .008" runout, the only difference was the shape, size was the same at 600.
Ever heard of chasing your tail?
Cheers.