This is exactly the same setup as in the GSXR's.
You can fool the TPS to thinking the valves are still there... or you can just unscrew the valves and remove them.
If you leave the rod etc alone then the ECU doesn't know the plates are gone.
I have entirely removed them (rod and all) in my GSXR and once you get the fueling right again you don't need a dyno to tell you it's quicker.
I really couldn't be bothered chasing up before and after dyno runs and crap to post on the net but the gains are quite good.
The biggest fueling problem on te GSXR is acually about 3500 - 4000 rpm when you remove the 2nd throttle valves. The custom map fixes it.
You get more power - EVERYWHERE
This is not a one off. It also applies to the 04-05 Yamaha R1 as well.
The R1 likes them removed even more than the Gixxer.
As I said, they are mufflers.
Kawasaki, Suzuki, Yamaha engineers know best ? Well they have to pass noise and emmissions test, I don't.
Why do you think Yoshimura sell kits to remove them and/or lock them open ?