A couple of things.
Fired brass will grow with each successive firing until you have a crush fit. For instance this is a typical set of measurements taken with the Hornady Headspace Gauge on a factory 30-06 rifle:
New cases - 2.040" (this is with subtracting the 2" of the gauge attachement on your calipers)
Once fired - 2.0485" (neck size only)
Twice fired - 2.050" (again neck size only)
3 times fired - 2.051" (slight crush fit)
4 times fired - 2.0515" (crush fit)
Notice that the brass expands ~75% on the first firing but it is not through expanding. What is happening is that the brass has a lot of springback when new and springs back ~25% on the first firing. Upon successive firing the brass work hardens and springs back less and less until it does not have enough springback to negate the crush fit. The amount of expansion and the number of firings before a crush fit will depend upon your load, your chamber, the brass and the shape of the case. You need to understand this to get a grip on what is going on.
Another thing is that you misspoke about neck sizing
"set up my neck sizing dies to set the shoulder the same as this case and be good to go"
Neck sizing dies do not set the shoulder back. A neck sizer will only size the case neck and not any part of the body or touch the shoulder. It will be a dedicated neck sizing die and it would be called that when you bought it. If you have a standard die then in all likelihood it is a Full Length Sizing Die and it will be impossible to size all of the neck without sizing the case body and having an effect on the shoulder (whether it pushes it back or not will depend upon how you set it).
So the question would be what kind of die do you have? It will say on the box.
"Since the brass expands and contracts, is there any point in adjusting the dies up some from the fired case measurements to get the shoulder against the chamber as close as possible without a crush fit, or just go with the data points I have?"
Normally I fire a sequence like the one above and keep records in order to find out where my chamber shoulder is. You will not be able to determine your shoulder position until you start to get a crush fit. There are short cuts but it will only get more complicated if we go into those now.
There is a way to partial neck size with your Full Length Die which is a way to keep your brass expanding until it has grown to fit your chamber:
1. Raise the ram and thread the die in until it hits the shell holder
2. Lower the ram and UNTHREAD the die about 3/4 of a turn
3. Size a case and it will only size about 3/4 of the neck which is plenty to hold the bullet
This will leave a part of the neck unsized close to the shoulder
You can do this until you get a crush fit and then when you set your FL die to push the shoulder back a little it will size the entire case. Lock your die and then when you resize next time you will be close to having it set to minimally resize your case.
You only want to push the shoulder back as little as possible to get rid of the crush fit. That will extend your case life.