The ONLY proper way to measure chamber runout is to pull the barrel from the action, indicate it in a lathe through the spindle bore, datum off the bore centerline, and then measuring how far off the chamber is from there along a few different spots, the shoulder area, mid case, and then the web region. If your stylus will reach, do the neck too. Keep in mind that the bearing cassettes in the lathe need to be nice and tight as well otherwise you'll just tolerance stack the dimensions and it won't tell you anything anyways.
(This is why I advocate chambering lathes with tapered gamut type spindle bearings ='s zero runout in theory)
Also understand that it is next to impossible (meaning, it can't be done) to indicate a barrel to .00000" If a guy gets it to .0005" he's doing real well. Some will argue this by stating that they shove gauge pins in the bore and then go off of them and then its easy to get the zero runout.
Perhaps. But you still have to have a clearance between the pins and the bore. You have to otherwise it'd take a hammer or press to get them in there. So, there's still a tolerance stack, however small it may be. That and I don't care to shove a 62-65 rockwell gauge pin in a precision machined/lapped surface that bullets travel down. I know me and I'd screw the bore up. When I indicate a barrel, the process is rather "kinky" so that I index the bore exactly where the bullet enters the barrel and where it exits. What happens in between I can't control anyways so I don't care.
I go right off the bore and indicate the "bumps" in the barrel. When I get to or under .0005" I stop and start making chips. Hasn't failed me yet.
I'd bet you'll find that using this method, factory barrels are out by even more than .002" in a great many instances. In fact, that'd be a good one.
Your cartridges, fire formed or not, are not qualified gauges or "castings" of the chamber so it won't tell you much.