So, Toyota just called me (a few days before my car is ready) and tells me there is no way on this green earth that they can put a CAl on my car with the supercharged. WTF? l KNOW you can put a CAl on a a tC with a supercharger, l know someone with one. So my question is....why is Toyota lying to me?
Ok if its not possible, because of warrenty issues. Can someone (perferably someone that works at Toyota) explain why?

They are not. The truth is they can not! It would void factory warranty there by making your dealer responsibe for any failures.

scion is getting fishy about there warantys here latley as well not wanting to cover things. the motor in my xb took a crap and they wanted my insurance to pay for it. l was 6000 miles away from end of waranty!! crazy. also there are 2 toyota master tech in my chapter od scikotics. they said if you want a cai do it after they install the sc and if there is any problems with it put the stock air box back in. hope this helps.

l have installed a Supercharger on a TC and it did say that a Cold Air Intake will void the warenty, it will allow to much air into and the boost can go to high causing motor damage.
You can do it, it is posable but not advised.

Scion is very proprietary since they are still in introduction stage. Prices for aftermarket are very reasonable and there is only 300.00 dealer profit in car. So use all Scion/Toyota parts.