In the above, you are talking about ARP recommending replacing bolts with .001 plastic deformation. Then right after you talking about elastic deformation, which does not count towards plastic deformation.
Quality rod bolts have a smooth barrel, typically not a knurled shank, that is pressed into a bore of the rod which centers it in the bore. The cap is then installed centering itself, on the two rod bolts. This is as precise as you can produce a rod. Quality rod bolts have spherical "dimples" on both ends of the rod bolt which index the micrometer or stretch gage.