When it gets line bored, the hole will be the same size. What they do is mill the bottoms of the main caps ever so slightly, and then bore/hone the mains to original specs. You're correct that it does move the crank up towards the deck, but most of the time it is so little that even the timing chain doesn't even need to be compensated. That is only my simple minded understanding of it. I'm certain that a sure enough machinist such as
@replicaracer43 or
@yellow rose could explain it much better.
