I have a completely stock B5, and have had no problems. I weigh 230+/- I set the preload on the shocks to the highest position, and the tires are both at 35 psi (sidewall says 36 psi) I haven't yet banged the muffler on anything. I do expect the stock muffler to fail, they all seem to rust through at the front at some point. If it happens during the warranty period, I'll just get it replaced. I wanted the EFI pipe, but it seems to have the same problem. I don't really care for the megaphone type muffler on the B5. It looks out of place to me. My '66 Bonnie had the peashooter pipes, later Bonnies had megaphones. Then the new Bonnie came out with peashooter type pipes, but with an awful kink in the header right before the muffler. Now only the T-100 has the peashooter pipes, the base models use megaphones. Also look at the pipes on the Kawasaki W650. That is what I want for my B5.
My main concern with the stock pipe is that being so heavy, and with all the vibration, the mounting brackets may fail, which would likely crack the head where the header pipe attaches.