I really don't want to buy something now to find out half a year later it wont work with the TRD supercharger.

Anybody have any insight on this?

 

If you look at the pics with the SC on the TC, it appears that the stock intake box is still attached to the engine. Since the CAI takes place of the stock box, it would be pretty safe to say "yes" to your question. Take a look at the pics under the "TC" section of Scionlife.

 

It looks like the airbox is retained, but it does not look like the rest of the intake is reused.

 

i don't think the AEM CAI is designed to handle the increased input of air for the S/C... usually forced induction has it's own setup to be capable of high flow intake.