I go off of the things that I have at my disposal to give my advise on this
The factory tells you it must be done, and from my experience at the dealers I have worked at, things as simple as changing your spark plugs have had bikes coming back with running issues. Another thing too, if you have to reset and zero the TPS at every service just to help the factory computer keep up with the changing parameters its needs while it wears over time, why wouldnt you need to do some sort of adjustment for putting on some sort of modification? Also wouldnt you want to see the most out of the modification by running it in conjunction with some sort of ECM mod? Yes, it will run, but in a lean condition. Depending on how you ride that could cause problems, maybe not right away but it could. If you want to take chances with your however many thousand dollar investment just to save some money, be my guest. I would rather keep it running in tip top condition and do it properly the first time.
maybebuell - yes on some of the big twins, we have seen that you can get away with it just doing mufflers, but not always on those either. I have had several of the people that "heard from their mechanic/buddie they can run them without a tuner/download". They are the same people that come back a short while later buying a tuner because their bike runs hotter and their new pipes blued up. I am just offering my inside insight to help you out. You can choose whether or not you want to do it with your bike or not, but what I am saying is the way that it is supposed to be done.