the reason why u see that is because the AT trannies sit closer 2 the A/C fan and there is very minimal space in there. I have seen ppl force the CAI's into the engine bay but it is a very tight sqeeze and those ppl had 2 do mods.
Install the Fujita M/T CAI in a A/T (not recommended)
there is the link to the writeup of how they did it. If you are looking for a good intake for the fit i recommend waiting for the T1R forced induction box from AJ racing. I know its not cold air intake but it does 11whp.

That kinda numbers is keeping me away from my CAI way's. Plus the intake is carbon fiber and it looks hella phat!