I think I would take it back to them and let them drive it and re-evaluate it. In the end, I would hope if the gears get damaged it would be on them to replace and if I was them I would want to correct it now before my reputation gets stained. Most things don't fix themselves as you know.
I've already taken the shop owner for a ride and he's aware of the problem. He's the one who told me to drive it some more and see if the noise quiets down.
