On the model A engine measuring piston protrusion when setting up for a high compression head.The space between the piston crown and head at TDC is called quench, and ideally it’s .040.. Fly cutting is relieving the head above the piston, that dimension is critical for factoring quench.
Measuring combustion chambers is interesting, but don’t be worried about a few cc deviation, the engine will run fine. It is important not to have too much compression, a combustion chamber too small effects valve ‘breathing’