It doesn't have to be, the cylinders are bored relative to themselves. Companies like BHJ make Block truing plates that you bolt to the deck like a torque plate that you indicate to replicate a more precision placement of the bores like the factory blueprint bore positioning and bore centerlines. But you run the risk of offsetting the bore enough that it won't clean up at a .030" bore size if there is a lot of ring wear at the top of the cylinder.
Since the cylinders are bored originally and correctly from GM, centering up on them will get you as close as you'll ever need to be. They used NC machining procedures when they made them also.
