It will not void your warranty. Go read the Magnuson–Moss Warranty Act as they cannot deny your warranty of the motor based on the exhaust system modification. Always remember no matter how "refutable" a dealer pretends to be they are all liars and scoundrels.
Now if the exhaust system fucks up then it is all on you. As for the M muffler vs the Magna-flow... The Magnaflow is to be honest the better buy because you will actually get a performance gain however... the M performance exhaust sounds awesome.