Shouldn't be any difference. The rear brake manifold is accessible, as is the rear caliper. There's no interference at all where the mounts attached. It may be easier to route the brake line, but the exhaust doesn't need to come off.

 

I have those controls on my 06 fxst. Best on the market at a reasonable price. Fairly easy install by yourself if you understand how to bleed the brake system. If you change your exhaust you may as well get a stage 1 kit and a power commander. You'll notice the improved acceleration right from the get-go.