Here's some of the science behind the design of an exhaust. I don't think English was the author's first language but its a good explanation.
"During each cycle of combustion, gas flow in the exhaust produced a wave of high pressure. It is logical to assume that a wave of high pressure should also produce a wave of low pressure. At some point in the exhaust system, which is determined by the designers, some of the waves collide. When the high-pressure wave leaves the tube, the wave of low pressure that follows it, is reflected back. A wave of low pressure promotes filling of the combustion chamber with fresh fuel mixture. Then the reflected wave of high pressure prevents leakage of the fresh mixture through the exhaust pipe. Next wave of her low-pressure scavenge the combustion chamber. The process is repeated, the bike is breathing evenly and well.
The length of each pipe exhaust system carefully calculated to pressure pulses were required to point at a given time. Properly executed release plays a crucial role in engine performance."
When you shorten the system, the pressure waves are no longer working to fill the combustion chamber the same way they were before.