ncgirl, I'm not a mechanic but have spoken to mine about the same issues.

I was told that since the whole SL timing/tuning system includes that CO2
setting, that a cat removal could require re-setting everything.
You may get a whole different airflow through the engine and that could
impact the fuel mixture.

I stress 'could' because every car is different. There's a section on the CO2 setting in the Haynes SL book - $15.00 max.