Does Line Honing change the crankshaft's centerline?

Not if it's done correctly. Done right, a very light skim cut comes off the block side. Not enough to change anything, but just enough to clean it up. The main caps are machined down a touch where they meet the block. Then the align hone or boring bar makes the crank bore round again and locates it correctly. When correctly done, it will move the crank center line little to none at all. A LOT of machine shops do not do it correctly, so sometimes you have to tell them how.....or find another shop.