Correct me if I'm wrong BUT ... its rarely an alignment issue but more a "fitment" issue. Once the block is bored at the factory things should not change. However, if you swap or machine the crank and you install new bearings then you need to align hone to achieve the desired clearance. This usually involves grinding a hair off the mains then line honing to the required size.

So if you take .010 off the crank on the mains and buy an oversize bearing, that's all fine and dandy BUT those bearings may have too little or too much clearance. Line hone is how this is adjusted.