Pretty sure you still owe the deductible on a comp claim, but it is upstanding of him to handle the claim that way. I don't know every policy in every state, so it's possible you have no, or lower deductible on comp. If so, more the better for you.
ETA: That is a crazy puncture. There is no way whoever was driving it at the time didn't know it happened. Not that it's helpful, but my guess is some salesman took the car to lunch, ran something over and just parked it without saying anything. I used to see that all the time when I worked at a dealership.
One time this guy was high on coke and totaled a car, then limped it back onto the lot and pretended like nothing happened. Haha.