For running stock crank and rods, I will usually get a rough bore done, bring the block back home, clean it and assembly at least 4 corners but typically all 8. Take readings then pick a cut number. For an aftermarket kit, I'll get the shop to even up the decks with as little cut as possible, then supply the deck measure to the supplier of the rotating assembly. With the current tech, they can spit out pistons to set the final deck clearance anywhere you like.