Freebore has nothing to do with the area of the chamber where the brass resides. There will be zero difference in a true freebore measurement.What would one suppose would be the difference if you used the Hornady case that comes with the device, OR
A Fired Case Unresized from your rifle or a Resized case for your rifle's chamber?
If using the boltface as your datum (Base to Ogive and subtract case length as a relative means) then a fire formed case bumped .001-.002” would be ideal. This will give you the most consistent readings. This will not give you a true freebore spec, just a relative contact point for your chambering. Which will be sufficient, if not trying to spec a new reamer or chamber.