Unless it damages the bike, it shouldn't void the warranty. You'll get crap from some dealers, but the bottom line is that if something falls apart and has nothing whatever to do with what you did, it's a warranty issue. If you change the pipes and the wheel falls apart... you know.
Even if it's connected in some way, say you change the pipes and then the oil pump fails and the engine eats itself, well... the pipes had nothing to do with it and Triumph generally covers that stuff, unless the dealer explains in detail to Triumph that there may be some aftermarket cause. Hell, dealers will sell and install aftermarket pipes (even the Triumph pipes marked "For Off Road Use Only"... right like you're going racing at Daytona or dirt tracking with those).
I think most everyone has done at least the AI removal and installed some other kind of pipes without a problem.