Firebob, if you had the block squared and just one piston was higher than the deck was the deck machined on a plane not parallel with the crankshaft bore? Or do you have one piston slightly taller than the rest? Or was the crankshaft machined with one journal greater stroke than the others, no that would give you two high pistons.

You could be correct about the reason for not zero decking, the machinist may have the block all squared up and doesn't think the extra benefit of zero decking are worth the cost of re-machining if it's not a performance engine build.