I should have updated this a few days ago, but I installed my parts. I was in a bit of a hurry, so I didn't get pics of the whole thing.
Even after removing the joint, a new bolt was tough to get started and tighten in the old joint, even though the threads look perfect, so I'm going to guess the joint gets deformed as well as damaging the bolt.
I'm thinking the alignment jig is simply to provide Honda with visual evidence this repair has been done properly. It's pretty easy to hold the bolt on the center of the groove while snugging it down.