Changing the pipes does not mean that you NEED to put in a fuel management system, but you may WANT to. The Yamaha guy is correct in that he told him "that he needed to add the power commander after adding the V&H 2-1 big radius to make the bike running correctly." The bike will run without one, but to optimize performance, you will want one. Read the first post in this thread. If you change the exhaust, you probably need to tune the engine, too.
Changing pipes without fuel management does not void the warranty. My dealer does it all the time. You will find many of our forum members are running that way without a problem.