Are you using the green plastigage?
Once reason I can think of that explains why you get .001" with the plastigage but the crank is locked: the rod ends and bearings are getting the crap distorted out of them with this very high degree of interference fit. If you have .030" under bearings, meant for a journal size of 2.094-2.095", and are tightening the rod ends onto a 2.109" journal size, then who knows in what direction(s) the rod ends and caps are going to have to give when you torque them down, and how the rod cap will distort. So the bearings and rod end/cap can be clamped hard at the sides where the parting line is located, and the rod cap bowed up with a bit of a gap where you are placing the plastigage.
If you do determine that the journal is indeed 2.109" + or -, then I'd be getting a bore gauge, torque down each rod and cap pair outside the engine without the bearing shells, and carefully checking the rod ends for roundness. (Or take them to the shop and ask them to check the ends.) I'd be concerned that some permanent distortion may have been put in the rod ends and caps.
OK on the source. Hard to say on the quality control there; never heard of issues (but I sure don't hear everything!). And yes the cranks are the same for those years; that's not the issue.