CAIs in S-Line mode should not have any problem. I used them in S-Line on my stock Z without a tune with no problem at all.
Technically you should not having issues in R-Line mode either with a proper tune. I "think" we were not tuning the MAF scaling correctly but, at the same time, I also don't know of anybody that has successfully tuned them in R-Line. I'd love to hear from them tho