Hey Steve, I doubt that complaint will be a big hurdle because in the end, they insured the guy and he was fully at fault. I had a similar problem with State Farm last year when a lady was kind enough to rearrange my Mustang's driver's side fender, bumper, wheel, and suspension to the tune of $15K...they complained a bit, but ultimately bit the bullet.
On a sidenote, I sent a client of mine to BOS. He lives in AZ and wanted to know if I had any suggestions in regards to body shops and Penny came to mind. I couldn't vouche for them personally, but you seem to be happy with them as well as a credible source, so hopefully it all works out.