First off the OP said it is a Pre- Fit.
Second, you can fire a case and make a modified case, and then remove the barrel if you want.
In my opinion it is more convenient to not have the receiver in the way if it is possible.
A Hornady modified case will suffice.
I always take a measurement, to the lands before I run the reamer in it's entirety- if it's a new reamer to check the specs.
Once the reaming operation is complete and head-spaced, I will take a final measurement for reference in my notes and relay to the client if asked.
This is all completed WITHOUT the receiver installed.
So my answer would be to take a measurement with the receiver removed if you have the capability.
In either case, you will accomplish what you are looking for.