Yeah i had straight pipes for 4 days.. popping drove me nuts on deaccel and shifts.... and yes im sure ur magnaflow will pop alot, if u listen to it on de- accel BONE STOCK u can feel it and u can JUST hear it popping... so any louder exhaust will just amplify them :S....
A magnaflow, corsa, jba etc catback does not make enough of a differene to require a tune. Its in the programming. Called DFCO (Deceleration Fuel Cut Off) and it can be turned on or off with the higher end programming tools (LSXedit/HPT).
Personally it doesnt bother me and the car made the same popping with the stock system although muted due to the resonator. Maybe with LT's it would but at this point (stock) its not enough to care. Besides its a high performance car, the popping goes with the territory.