That's a very good question to which I don't have an answer that might help you. I do know that the Nismo exhaust is less restrictive than the standard GT exhaust for example. In your case, I'm assuming having a custom system means yours flows well, so the Nismo back box would be the way to go. I also assume that both the standard box and the Nismo one fit in the same way, but I'm unsure exactly, as I have only had the car a few weeks and the Nismo was on the car when I bought it.
I can tell you that the Nismo box is very quiet, so mush so, I'm going to change it for some Tarmac Sportz short tails. I'm also unsure whether the previous owner put a full Nismo on or just the rear box. This will all be revealed when I get to Tarmac