Kyle,

Picture that the piston is round, but the chamber is oval (roughly). Therefore there's a part of the piston that faces the flat bottom of the head, and if the piston came up too high there'd be contact (a Bad Thing).

So, say the head gasket crushes down to .050" and the pistons come up even with the top of the block (numbers for illustration purposes only). The piston-to-head clearance is .050". Shave the head as much as you like and it's still .050" and the squish/quench is still the same, although you've raised CR because the volume of the oval cutouts is smaller.

In this case, if we wanted the clearance to be .030", there's two ways to do it: 1) use a .030" gasket, or 2) deck the block so the pistons stick up .020" out the top. Now we've got the tight squish/quench, AND we've raised the CR a bit, but not a whole lot. Only now can we calculate how much more volume to take out of the oval cutouts by shaving down the head.

See? Ideally, we want zero clearance without contact at maximum revs and maximum temperature, but the pistons and rods "stretch" with heat and revs, so we need to allow for that and build in some clearance measured with the motor cold and at rest.

Two real-life examples... my MPPE motor has a 93mm bore (2175cc), so that means using the Elring big-bore gasket that only comes in .050" nominal thickness, and crushes to .047". I wanted .032" clearance, so the block is decked so the pistons stick out .015".

Now I'm putting together a 2036cc motor for a guy (only .040" over), so I can use a .030" gasket that crushes to .028". For this one we want .030" clearance (it won't rev quite as high so a bit tighter is safe), so we're cutting down the block so the pistons end up .002" below the deck.