i have seen this kind of damage on bearing due to an engine that DID NOT START IN 2-3 REVOLUTIONS on initial startup.. because of improper/lack of FUEL..CORRECT SPARK AT THE RIGHT TIME or WEAK IGN...ENGINE MUST START IMMEDIATELY!...
I'm by no means a pro engine builder but I'm thinking if your rotational clearance off the caps exceeds crank fore and aft motion, you're probably good.
Evidently you are not comfortable with the cap mismatches and I probably wouldn't be either.
Well, try to move one. On the #4 cap, it appears to hang over the block. I might try to reposition this one just to satisfy myself. Don't forget the assembly lube.
When I assemble the only cap that gets centered is #3 for the thrust. I do that one first. Put the cap on, finger tighten the bolts, then using a soft faced dead blow hit the crank fore and aft in the block a few times, then torque the bolts in 3 steps. The others - as long as the bolts go in easy, again, finger tighten them, torque in 3 steps. The bolts you have are fine, but if you want to replace them any 360 used bolts should be fine too.