Well, the MOPAR CAI I've seen is an open filter type. I was referring to the AFE Stage 1 and Stage 2 intakes (sorry, I could have been a bit clearer there) and those are a cone type within a box. So yeah, they are a bit different. Both will work just fine!
If ya don't want any problems, and my dealer has none with me even though I have the AFE and exhaust on it; then make sure you return your vehicle to stock with the programmer. You can always re-install the tune after you get the truck back.