My personnal feedback :
The Bypass is not designed to be used with stock mufflers and there is no tune available for that set up.
Anyway, Bypass + stock pipes works without problem.
I've never understood why so much people uses that set up because the stock mufflers are much more restrictive than the cat.
I've road tested the two combinaisons :
Bypass + stock muffler
Cat + aftermarket mufflers (Tor's and Maddogs)
The sound is about the same for both with the tor's. (A little bit Louder and deep with the Maddogs).
About performances, the cat + performance mufflers is much more pleasant to ride, with more torque in the bottom range than the other setup with better high end.
Good point : A specific Triumph tune is available for that (everybody doesn't want to go for a PC III or a tuneboy....)
I still believe that bypass + stock mufflers is a nonsense and that your dealer is not as idiot as he seems Rude dog !
Only my two cents........