[Jeff Lee]

My impression is that if the specs call for a negative deck, then the piston had better be below the deck of the block. At this point the gasket is not part of the equation.
The opposite is true if the specs call for a positive deck; the piston had better be above the deck of the block.
How much above or below the deck is not the issue as long as the blueprinted engine meets or exceeds the specs; more clearance is allowed, not less clearance.
Since your spec is .002" (below deck) then you'll have to machine the big end of the rods to pull the piston down to where it needs to be.

Note: this is the same issue as the rocker ratio rule. The end result is not the answer, getting there using the specs provided by NHRA is the requirement.