Cold Air Intake is a misnomer, most of them move the intake from in front of the radiator to deep inside the hot engine compartment. Most if not all are compatible with both transmission types. AFAIK there is no compatibility concerns with the transmission and these intakes. But a lot of the information on them maybe just hype. Mostly they change the sound of the vehicle.
I'm using this one. Had it for about 5 years now. Just put a new dryflow filter on from the site recently. Been re-cleaning the oiled one it came with when I got it about 5 years ago. I have zero intensions to replace this intake any time soon. It performs amazing, sounds amazing, looks amazing, and it helped my MPG. It mimics the factory style so after some research (long ago) I decided to go w this one. No disappoint. AFE TAKEDA INTAKE SYSTEM 11-12 HONDA CR-Z L4 1.5L STAGE 2 PRO 5R WRINKLE BLACK