Yes, your assumption is correct. Up to a certain level of boost (~20lbs) the factory does not present any restriction, so it makes sense to keep it in place. It will certainly help keep the low-end torque in play, but there really is not much lag with the twin 61mm turbonetics units I am going with anyway.
Here's the dyno sheet of a 2008 GT500 that has the same setup as I am putting on my car:
I have not heard of any overheating issues. Not only does the system use the factory intercooler, but it also comes with a second air-to-water intercooler to help keep temps down. I'd be more concerned with blowing out the seals of the blower at high boost levels than I would be things getting cooked.