Does Line Honing change the crankshaft's centerline?

Actually, yes pretty much you can. I outlined the procedure very clearly in an earlier post in this thread. Would you consider .0015 (sometimes less) removed from the block side moving the crank center line? It's all relative, because as YR and others mentioned, the block has to be "close" as far as main saddle alignment to begin with......most of them actually are. That's the whole purpose of removing material from the caps where they meet the block. That way, you remove most of the material from the CAPS, virtually leaving the block alone with only the lightest skim possible. This effectively leaves the crank center line the same.

0.0015" is a significant amount when you work with machinists all day like I do, but as I said, it's nothing in terms of a timing chain set.

I've never seen a block blueprint so I don't know what the production tolerances are, but I can't imagine this being beyond factory tolerance!

Edit: I've also always wondered how close to true centerline the main cap surface actually is. It could be off quite a bit and still work.