Deck height of the block is determined by measuring the distance from the top of the block to the centerline of the crank journals.
To lower the deck height for a zero deck piston height, the machinist needs the piston to determine the piston height. The height is or should be always listed by the piston maker. As with above, the height is measured by going from the centerline of the Pistons pin to the top of the Pistons fiat spot on top, not the dome if equipped. This is also measure along with the rods to be used.
The machinist could measure everything or he could bore the block and fit the Pistons to the rods and then to the crank and rotate it around and measure the distance left above the piston.
I like the second method with all 8 Pistons in the block. This will quickly show if the deck is what it should be, even, flat, level, un-twisted, tilted, warped, bowed or bubbled.
Other machinists will square up the block (you must request this.) and go from there.
I have spoken with a few ace machinists and it seems to be what ever they like.