Checking the dome volume is done by pushing the piston down some amount deeper than the top of the dome. Then measuring the amount of liquid required to fill the cylinder to the top.That amount is then subtracted from the calculated amount that would have been required to fill the cylinder, if the piston would have had a flat top.This takes care of any eyebrows right away too.
It is common to select 1/2 inch down, or 1 inch down, as may be required to cover the dome.The measure must be exact, and must not move during the process.
On a 3.66 bore, each inch is 172.406cc, so an error of just .006, would introduce a 1cc error in volume, so be careful.