If it doesn't have the stock flange on it now then they'd react the same way. As long as the catalytic converter is there I don't see the warranty being voided though. Say you put on a cold air intake and your something happens to your engine, unless they can prove that the intake caused the problem they have to cover it. If they do prove it go to the manufacturer and tell them they're product broke you're car and they're going to fix it.
2006 Red Chevy Cobalt LT
mods: Kenwood DNX5140 Head Unit, HIDs, Halo headlights, LED taillights, Injen CAI, LSJ throttle body, 2.4L intake manifold, red interior LED's, TWM short shifter, custom fit red seat covers, red trim and door handles, SS gauge cluster, Racing Solution long tube header/downpipe, Corsa touring exhaust, lightweight crank and alternator pulleys, trifecta tune, 17" Motegi black rims