If you really want to find out where the differences in your piston deck heights are use one piston in the four corner cylinders and rock that piston back and forth in the bores and use your depth mike or dial indicator directly over the wrist pins and see how much variances you have wrench scope
Please let us know what you find out thumbs
I see this often with all after market parts, usually it is the rod scope

Mr.Cab Racing and winning with Mopars since 1964. (Old F--t, Huh)