I don't think any specific reason was ever given. We know that in the original tune the emissions equipment was shut off in situations where it would otherwise reduce the longevity of, or cause damage to, engine components. So when the EPA forced them to turn the emissions on, they had to adjust...
If your buddy paid 3k to fix this, I feel sorry for him. I think the dealer shafted him.
I know of several, myself included, on another forum that have had the flange bolts fail. Most of us noticed the failure because it causes the exhaust to whistle at higher rpms or under heavy load. Granted...