Had something similar happen to me (not a warranty claim) and my insurance *maybe* went up like $10 a month. Definitely not the end of the world if it was, indeed, a road hazard incident. Much better than paying $6k out of pocket.
At first I didn't remember "hitting" anything, and was pissed when the mechanic didn't take blame for what I thought was their error. Then I remember scraping backing out of my driveway a little too straight (steep curb) and it turned out to do about $2k worth of damage to my car, messing up some stuff in the front end and knocking my intercooler loose. This was in my 335i.
Also, Op, if you hit something odd shaped, even like a tire skin from a semi, it could do some strange damage.
Finally, if it's just a differential bold, that doesn't sound like something that would be that big of a deal to fix. If they provided a $6100 bill, perhaps they feel the other "damage" is worth/necessary fixing.