hows is a aftermarket pipe better than the stock pipe gutted?

 

An after market pipe is a "tuned" exhaust, designed and built specifically for your quad. Designed for the best flow and backpressure of exhaust to help with torque and power delivery.
A gutted stock muffler is just a POS gutted stock muffler that makes your quad louder and does nothing for it performance wise.

 

These motors do like a certain amount of back pressure also. Gutting the stocker is one step removed from running without an exhaust at all in many cases. My little brother had an xr650 and gutted the stock exhaust. I rode it before and after, on that machine it made a LOT more noise, yet was noticeably weaker throughout much of the powerband.

 

even with just the silencer out?

 

Taking the silencer out is even worse. All exhaust are engineered to perform a certain way. Even stock. Taking the spark arrestor out will open up the stock a bit. Taking the baffle out screws the flow of the exhaust all to h3ll. Taking the silencer off and running a straight pipe?!?! That's not smart at all. It adds NO power and will burn up your quad.