most all of us do not think in centerlines when we are trying to make a good case. An imaginary centerline right thru the center of the case is your true gauge line that will never change. Then you cbase everything off that line. The shoulder to base should be based off a gauge line (books like to call it a datum line, but that is incorrect in precision measuring). There are specs that call out a diameter for the gauge line point at the shoulder, or you can simply develop your own diameter and use it. I prefer to split the difference between the neck O.D. and shoulder O.D. Finding the correct headspace number with that method is not hard to do, and you really don't need any serious measuring tools. Just a good digital caliper and the correct bushing for the shoulder is all you really need.
The folks here that happen to own their own chamber reamer may even have a print showing the gauge line data on it. That's a good start, but after that your at the mercy of the gunsmith's chambering job. If a go gauge headspaces in your chamber about right then your home free, but if not you got a place to start anyway.
Don't let the issue beat you up, cause it just ain't that hard to do.
gary
...never mind the fact that the case head to body aren't perfectly square on virgin brass and you may be dealing with banana cases to a small degree even after firing in the perfect chamber due to uneven case wall thickness, all of which assumes your chamber and bolt face are true and concentric to begin with as you pointed out.
I think I'll stick with the HNL comparator to get a workable setting for my dies and then spot check just every now and then to be sure there hasn't been any meaningful drift.
One option might be to use your reamer to make a die which could sit neck down on a flat base and then use a flat/square ground disk on top of the case head to measure with an indcator. That might mitigate the effects of the ellusive centerline much like your Wilson seater doesn't have to be dead center under the arbor press. ...a simpler, home made version of the the Redding Instant Indicator. But, you don't fire your ammo in a die or in a Redding indicator. You fire it in a chamber made from a particular reamer as you pointed out.
It really comes down to what you want to accomplish. If you're out for speed/efficiency, then indicators are faster/easier for me than calipers and mics. But, I don't check HS on every case.
If you only want to be within a thou, then calipers are pretty easy to spot check.
If you want to go to tenths, then I suspect you need to reasses not only the measuring apparatus and technique, but the general behavior of brass (temperature, spring back, settling, work hardening, etc) as well as your process for sizing and staying within your desired tolerance which may or may not have a bearing on precision shooting.
-- richard