The reason for the align honing after you change fasteners is because the main bore is machined with the original fasteners. The final bore shape is set when that particular fastener is preloading the block and cap. When you change the bolt, use something stronger, or go to a stud, you change the amount the bore distorts, and thus change the shape of the bearing bore. When going bolt to bolt, it's not much of a change simply because the material of the fastener makes little difference in comparison to the type of fastener. When you change to a stud, it preloads much differently and can distort things so much that the bearing clearance is affected.
If you are at all familiar with the horrid quality of the factory machining, and can appreciate a true performance engine, you'll have every block align honed regardless of new bolts or not. I have yet to find a factory one that did not improve at all by haing it done, and a good shop's equipment needs the main bore to be perfect as it indexes off it.