First, I will say that I prefer the FRPP/Whipple(or any twin screw, for that matter) to the Roush. But, if you have a Roush car I can see why you would want to stay with that theme.
I'm a little confused whether the warranty you are referring to is for the supercharger itself or for your Mustang's drivetrain. If your dealership will install a Roushcharger and warrant your car at 6psi, that is a good deal. I would look at the FRPP S/C that is due out in the next few months as a Super Performance Pack and ask if they will offer the same service and warranty on that. If so, that would be my choice. Unless, like I said before, you want to have all your equipment from Roush, which is understandable. My point is that you may have other (IMHO better) options.
Please keep us all informed. I'm sure there are other guys that would love to know where they can get this type of work done under warranty.