Listen to EVERY high performance engine built. They ALL pop when closing the throttle.
It's in the nature of the exhaust. Being more "free flow" in design it can not "muffle" this pop.
What is happening is there is always unburnt fuel in the pipe. (that's what cats are for). this fuel does ignite every time the exhaust opens. With an open pipe design you can here this fuel burning. A closed pipe masks the sound. That's all there is to it.
Old school chopper guys purposely run rich to amplify the effect.
You can minimize the pop by getting your combustion as close to perfect as possible but you will have to balance your jetting/needle height or injector duration/pulse width to gain perfect combustion across the rpm/load range.
Only experimenting will yeild results, and they will change with weather conditions, road conditions, and even to some degree the brand, and state of your engine oil.
Embrace the pop! Become one with your engine! I am your father Luke!