I found this online at american muscle, what does this mean?

A Note On 2005+ GT Cold Air Intakes: On 2005+ GT Mustangs we must have the actual brand and model of the aftermarket Mustang Cold Air Intake being used. The 2005+ uses an advanced PowerPC processing unit instead of the old PCM systems on 2004 and older mustangs. The new system is VERY sensitive to airflow changes and most 2005+ Mustang Cold Air Intakes use the stock MAF electronics but change the actual MAF housing size greatly distorting your MAF Transfer Function. This is why you can not tune for cold air intakes on 2005+ Mustang GT with a strategy tuner such as the Predator or the 9415 Xcal2's.

 

I think this is what they are getting at...
You can't just add or remove spark or fuel with the strategy tuners and have everything work correctly.
If they know which intake you have, they have the software to load a tune into the tuner so it will be pretty close to right.
A dyno tuner can tweak it to where you can be sure it is running safely.

 

The Spanish Oak ECU in the S197 has been tuned to be VERY picky about any changes in the baseline. Thank the ever tightening emission regulations for that!

So, when you DO make a change that impacts air flow into or out of the engine to any significant amount, it will throw the car out of that little window. When means the tune has to be adjusted to shift the "window" back to the right place so the ECU stays happy. This window is small enough that even differences between different CAIs can be enough to **** of the ECU.

The days of quick and dirty tunes that the car just lived with is pretty much over. On the bright side, if they can get their tune dialed in well enough to keep the ECU happy, the drivability should be good enough to keep YOU happy as well!