What I do is the same as you, except I will rotate the piston to tdc, then carefully put an indicator on the rod or rod bolt, then push the piston up by hand till it makes contact with some part of the head, then record the reading. In the past with the .040 fel pro I have had a clearance issue and had to slightly machine the domes down for clearance. This would easily be rectified with a slight change in head gasket. Having said that, the piston manufacturers seem to have gotten a lot better in regards to these kinds of problems.