For the MSP, even a stock replacement IC is dyno proven to increase hp, but the vendors have never reported boost increases. I disagree with the boost argument, because full exhaust is legal in STX while boost control is not. I know for a fact that when you replace the exhaust, mainly going to single high-flow car versus 2 chocking cats, you bump up at least 1psi (~2.5psi in my case).
My only guess is that they disallow it because everyone has an exhaust they can toy with, but not everyone has an intercooler. One of the major rules I have a problem with is the CF hood. It should not automatically put you into SM. My thought is it should bump you up a single tier. Like CF hood on DS car should go to STX, CF hood on STX should go to DSP, etc.