I did not put the bolts back in. I did pack them with some foam I had around the garage, because I didn't want to dig mud out later to reuse the holes.
Hindsight, there are a few other holes that are down there that are left open from the factory, and those don't seem to clog with mud. So, do as you want.
Nothing (ad)ventured, Nothing Gained
Everything you want is on the other side of fear.