The silencer length is considerably less critical than the header length or total exhaust length when it comes to tuning an exhaust (and pipe diameter or course). As Maxwell implies, the silencer is just that, a sound deadening devise.
Trouble with two-on-one side setups has always been each pipe from port to outlet is going to be a different length (unless you have a collector box, a 2-1-2 setup, or have loads of very expensive serpent-like bends to compensate). Each exhaust valve then ends up operating under slightly different conditions (scavenging and back-pressure), resulting in loss of torque and consequently power. I seem to remember the very first Metal Mule 2-1 system (very unequal length headers) supplied to Damian I'Anson (ex Bike magazine) for his Himalayan altitude record attempt lost midrange and had various other "holes" in the torque curve, which he could only partially correct with a Power Commander on the dyno, and put down to the header design.
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