Are they the steel shim gaskets? If so, that's the answer as to why the pistons are down the bore, to maintain the proper piston to head clearance (squish) of around .040". Squish is an important part of power generation and detonation control and the engines were originally designed for the proper amount of squish.
When switching to Fel-Pro or other composite gaskets from the steel shim gaskets, the deck should be surfaced by the amount of difference in the thickness of the two gaskets in order to get back to what the factory designed. So, if you have .020" thick steel shim gaskets and go to .039" thick composite gaskets, the deck should be machined down by .019" - which results in zero-decking the block. Other engines have the pistons sticking out of the bore by as much as .020" (or more) to compensate for head gaskets that are .060" thick. Why are the new gaskets thicker? Because they seal better.
The squish effect: the distance between the piston and the head closes up as the rpm goes up and the rod stretches. The squirting effect of the close tolerances speeds up the burn so much that no extra spark advance is needed above about 3000 rpm (depending), even though the time available for the burn can be as little as half (6000 rpm). I've used as low as .032" on a short H-beam rod engine without contacting the head at high rpm (7500) but the minimum clearance varies with the rpm, rod length and design. An aluminum rod engine needs an extra .020" - .025" between the piston and head because of the stretchy rod.
If you're not going to use steel shim gaskets in your engine ever again, there is no problem with decking the block for composite gaskets and using pistons with the stock compression height.
Some piston manufacturers do offer pistons for certain engines (SBC for sure!) with a higher compression distance to achieve a zero-deck without surfacing the block. Such a piston for a Pontiac 400 would have a compression distance of 1.735" (1.717" + .018"). Or use steel shim gaskets with the regular pistons like the factory did.
To think that all this zero deck stuff is because of the later, thicker, gaskets. There's no doubt that cutting a block the same amount as the gaskets have grown is a 'wash'. Makes you wonder why it's not mentioned by Jim Hand or Cliff. It reminds me of a Neurosurgeon recommending back surgery. Now I can throw a monkey wrench in all of this. I have the thicker gaskets on a stock build without any problems. If I pull my heads and use the original style thinner gaskets I can expect to gain what(other than a leak LOL).???? Would my engine run a tad cooler? It does creep up to 210 on a 100 degree day when stuck in traffic. Honestly, it's no fun driving the convertible when it's 100 degrees in traffic anyway.
