If it comes out of the gun crooked then it's the chamber.
Before changing anything, get somebody else to verify what you are measuring with their own equipment.
I'm not understanding how a chamber can be crooked, unless you clamp the action in a vice and bend the barrel back 180 degrees.
The chamber is made from a reamer. A reamer is one piece. If the reamer was bent, it would be un-usable.
The only way possible I can think of to produce a crooked chamber is to cut the body only first, without the neck being cut, then go back with a different tool to cut the chamber neck, and remove and replace the barrel incorrectly on the lathe between tool cuts.
Which is impossible, because chamber reamers are only ever one piece.
How does a chamber get crooked ?
I understand how a chamber may not be perfectly aligned to the bore, but not how a misaligned chamber "bends" the brass. The chamber is straight, why does it "bend" the neck ?
Runout on fired cases is normal. Chambers are cut to different tolerance, and fired brass will have runout. Two pieces of brass fired in the same chamber can have different runout.
The measuring of runout with the concentricity gauge is indicative, not actual. Your finger pressure rotating the brass induces runout. Press a little harder, and see that dial move further. True runout is measured on a lathe, and is limited to the runout of the lathe itself.
If you fire brass, and your runout gauge says 4 thou, then size your brass and your runout gauge says a different number, you only have a comparison between what it was, and what it is, not a true measurement.
I'm sure the experienced machinists have a chuckle at us when we talk about mechanical precision and these hand operated tools in the same sentence.