Piston pin height (compression Height) can change from different piston manufacturers. You may have an engine that was rebuilt at one time and "rebuilder" grade pistons were used. When replacing them, be sure to check the spec on the compression height to be sure you get them as high up in the hole as you can. Then you can decide to deck or not to deck and what thickness of head gasket you want to run.
One good thing is that the block must be pretty square. If you checked all 4 corners with the same piston and rod and it was the same , it must be square. Also by using the same piston/rod to measure all 4 corners you removed any variance from the measurment than could exist between the entire set of your rods and pistons. Good lookin out.