Ok - I get what you are saying - I decked my block to reduce the quench on my combustion chamber to .045 and then milled the head to get it flat and normalize CCs/chamber. I don't have stock pistons - I wound up with 9:1 compression ratio which is fine.
Decking the block without cutting the pistons would result in higher compression than if you did cut the pistons, but if you decked it so far as to cause a crash, I can see where you would have to cut the pistons. Thanks