Its not that big of a deal and leaves room for ugrades later.. Youll still gain witrh a properly designed 3" piped exhaust. Myself or any other s-chassis owners Ive talked to had anything bad to say about the apex-i N1 that is 3 - 3.25"
The torque loss is minimal if that , and iirc is only in certain area of the bands in our cars as well. Its been a while since Ive seen a dyno sheet of stock vs N1, so I cant be more specific.
I would be more concerned about the design of the unit then the 3" piping.