If the tube lengths are altered, the waveform of the exhaust changes. The goal is to have the timing of the wave just right, for when the exhaust valve is open. Think of it as if you were swimming in the ocean. You want to take a breath while you are in the low point of the wave, not as it is about to smack you in the face. You do not want a mouth full of water.
Proper breathing makes for a nice swim.
Proper exhaust timing makes for a nice running engine. I guess it is never fair to say that the mechanical nuts and bolts of this sport do not matter. Most of the time, the winner does have the best car. I do think that this weekend at Sears Point, the car may be less of the equation as in most races. If Gordon is not a factor on Sunday, the question of what made the No. 24 team great in the past may be answered.