This is a shining example of what I've been talking about on warranty claims!!! The dealer doesn't give a RAT'S A$$ about the Magnusson-Moss Act, or proving that the exhaust caused the problem!
They blame it on an aftermarket part and refuse to fix the problem under warranty. Your options are to actually take them to court and pay out of pocket to fix the car, or take the car to another dealer and hopefully they'll be more reasonable.
Since most people don't have the time to take the dealer to court, they win and they realize this.
Theory is nice, but it's not reality... Be very careful when modifying your car...