I'm no machinist, but that sounds like A LOT of warpage to me. I might be wrong, but half that seems like a more realistic limit.
I agree that .003" sounds like a lot, especially when the cylinder head flatness spec is more like a third of that, but I think you have to think about the overall blueprinting of the engine. if you don't want to count your time, you could deck the block until it's way tighter than the spec. You could also cc each combustion chamber, and port/gasket match, polish, etc etc etc
When I think about potential block warpage on an IDI, I feel like the head gaskets and heads tend to respond to most of terrors of overheating. If you have the skills and tools to measure and flatten the deck, do it. If you really want it machined perfectly, contact Justin at R&D or find a reputable machine shop and spend the money. if not, I'd abide by the seemingly large tolerancing that you have per the manual with the comfort of knowing that somebody came up with those specs 40 years ago when your rig was brand new.
Any any case: bullnose 4x4 crewcab IDI is an awesome foundation, so best wishes regardless of how deep you get into the build.