Bottleneck cases headspacing on their shoulder align bullets in the front of the chamber equally perfect up front in all chambers. Doesn't matter how the fired cases are resized as long as there is at least .0005" clearance around the case.
Get rid of that expander, deprime cases before cleaning them then use a bushing 3 or 4 thousandths smaller than loaded round neck diameter.
Bullets don't need runout under 1% of bullet diameter.
If you say so---my dies (both) are made when the chamber is cut and the brass is perfectly prepared. Factory chambers and commercial dies are a crap shoot. There are tools that allow for correction of this problem. I don't have the link anymore but use the tool as modified with a more precise gauge.
Found it:
http://bulletin.accurateshooter.com/2010/10/hh-concentricity-gauge-bullet-straightener/