Depends on the skill level of the tuner. If all they are doing is just taking the transfer values and plugging them in, and if the CAI is deficient, then ya you would see some irregularities. Tuning around it though is never a good thing, because then the vehicle isnt running 100%.
The transfer is basically the product of an equation that changes what the MAF sensor should be expecting in voltage and translates that into airflow.
Since you are enlarging the MAF housing most of the time when switching CAIs a new transfer value has to be inputted into the transfer table so the sensor knows what voltage equals what air flow.
This is my best laymen description.
If the transfer is off or if the CAI produces uncalculatable (if thats even a word) values, the final voltage/airflow reading will be off and the car will either give too much or not enough fueling.
For the copperhead pcm equipped vehicles, the wideband o2's in the rear can correct this to a point, but remember you have a MAF reading faulty up front, then the o2's reading properly in the rear. So it then becomes a continuous cycle, then a code gets tripped in extreme examples, or you will fine hesitation, surging etc at idle, wot, cruising.
Some of the problems with using SCT as a logger, is it is not high speed logging device to catch some of these values in a finite resolution, like say a Cardaq is.
You also have high and low injector slope values as well that can play a role in this.