In teh picture above, in the middle example where you have skimmed a slice off, in reality all you will have done is dropped the whole head down "X"amount. The point where the piston meets the flat squish roof will be in EXACTLY the same place. The top of the bore (or block if you like)

When you add the plate in picture 3, you actually RAISE the head by an amount.

Does that help?
Maybe if you see where the squish area is on a YB cylinder head?