Basically the heads sit flat... there's no "dome" in them. If the block was decked the pistons are pushed up farther and closer to the head. There is basically no room in there as it is, and the gasket is what is creating that gap. I believe the pistons protrude from the factory so they have to be really close to hitting before any machine work is even done. I know .008" is a rough estimate to the max that can be removed from the heads before there is issues. I know the Ford tech that was supposed to do mine told me if it went over .005-.006" he was going to order me new heads. Ford actually says the heads can't be machined at all, though most of us do it. I'd go with new heads personally. .012" or more off is a decent amount of material. Sounds like the shop did the right thing by adjusting the valve stem height, and sinking them in the head a little more.
If Kevin is right, and the block has been decked but the pistons weren't touched, that could be the issue right there.
If Kevin is right, and the block has been decked but the pistons weren't touched, that could be the issue right there.