That's not always true. All cars/bikes experience a backfire/pop through exhaust but you won't hear it due to the factory muffler and/or catalytic converter.
The reason my Busa is shooting flames is because there is no fiberglass packing to absorb it and I don't have the pair valve plugged which allows fresh air into the exhaust. If I plug the pair valve then I will reduce the popping through the exhaust. So, basically my Busa has a straight exhaust.
Did you Dyno it before and after you cut them?