I've worked (and am currently working) in the automotive service industry, both for independents and a dealership. The unscrupulous dealers will have issues like this where they get techs that don't want to be bothered to diagnose properly and tricky service writers that will (up)sell the excessive or unnecessary repairs that result. What does surprise me a little is the rate the man paid for his pebble to be removed from the moonroof. A minimum of 2 hours charge is a bit steep with a shop rate that's around the $70 per hour seen here. I doubt it took 2 hours to fix, and in the name of honest service and good will a really great shop would charge 1 hour at most or even do it free.
The shop I work in now has done as much, because it's right. You'll be paid well for such negligible 'free' work, with repeat customers and an excellent reputation.