I see this referred to a lot. Any machine shop that align hones or align bores a block that has not incurred damage, but only to bring the crank bore in line and then makes the block require a shorter than stock timing chain, doesn't know what the heck they're doing.
The proper procedure is to remove the main caps and remove a small amount of metal from where they meet the block. Usually this is .010" or less. Then replace the caps and do the realignment. The key is to remove more from the cap side as to keep the crank bore in the same or VERY close to the same place to vertical. This way, only a tiny, tiny amount is removed from the block......only a "skim" cut if you will.
That is the correct method and if you find a shop that will not do it in that way, run.