Pretty much, if you're looking for 500hp, you're gonna have to change something, and perhaps cause a warranty issue.
However, that said, you're much closer in the Cobra, and the internals are built to handle far more power. I'd feel better putting a bigger blower on an engine already so equipped. Consider all of the DSM guys putting bigger turbos on their Lasers and Eclipses, or the SVO guys running more boost in their turbo 2.3 Mustangs. If you strapped even the stock turbo from an SVO onto a non-turbo engine, you'd probably burn a hole in your pistons or snap a rod in two before you got much excitement out of it. The engine is just built to handle extra stresses and then a reliability factor. Warranty hopefully wouldn't be as much of an issue as it would probably be less prone to breaking, even with a slightly less than optimal tune.
Someone looking for stock Cobra power, and power alone would definately be better off buying the GT and strapping on a blower... definately.
JS