Hopefully Ken wont mind me inserting my 2 cents here. In order to promote more complete combustion and reduce detonation, experienced engine builders strive to have the clearance between the piston and cylinder head as tight as possible at TDC. This is known as the squish area, and tight squish squeezes the air/fuel mixture out of this area as the piston reaches TDC in a turbulent manner enhancing combustion. As our head gaskets are approx. .068" thick compressed its necessary to have the piston "proud" or above the block to create a favorable squish zone. From here its mathematics, from the compressed gasket thickness, of say .068" subtract the desired squish distance, say .028" and you get .040," "proud" or out of the hole. These numbers are just my examples, but hopefully can shed some light on your question.
Thanks
Randy