Magnaflow competition includes everything aft of the cats (overaxle and axle backs). You do not need a tune for this, and therefore, I don't think you'll have a warranty issue (up to the dealer really). You can add an off road x pipe. This will net you some power, but will require a tune due to the lack of O2 sensors. Any tune voids warranty.
In reference to your earlier question, catbacks give you a tiny bit of power, axlebacks are really for sound only. Idk about the V6, but I believe the 5.0 gets the most power gain from an off road mid pipe.
1988 GT - Stock
*SOLD* 2012 GT Premium, Black on Black, 3.55 Axle, HID and Security Package, Pypes Pype Bomb Axle Backs