I have the CAI with the poly tube and the flashpaq, works fine for me. I didn't notice any performance decrease when putting that CAI on.

 

I did get a response from SC on this and it is a legacy thing that is applied and for MAF based systems it does matter. CAIs on the Chrysler platform do change how it runs but not enough to effect the SC tuning.

I too have a poly based tube CAI (Airaid) and I have no negatives to report with it or when I switch back to the stock airbox.