On a full length pipe, you cut the header down, and the header ends where the pipe starts.

On a mousse can or other "quarter wave" pipe, the header actually does extend almost all the way through the can, and it's not cut down. If you cut the pipe short so it ends just inside the can, it won't work, you won't have a tuned exhaust, you'll have an expansion chamber muffler again.

The reason for this is the pipe coming in to the can creates a longer area for the pressure wave to develop, which is necessary. The pressure wave actually comes out of the pipe then reflects inside the can outside the header, towads the "top", then back. Basically it makes U-turn out of the header and back to the front of the can.

If you take apart an ultrathrust muffler or a Jett muffler, you'll find an inner bit of tubing in there doing the same thing. This inner tubing is what makes it "tuned" and not just a big muffler.