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Exhaust systems do alter the power delivery when installed correctly - even at part throttle. The entire system needs to be considered from where the air enters the airbox to it leaving the end of the silencer. Before this, a decision needs to be made about the way the bike will be ridden.

For example - by changing the expansion chamber, jetting , and adding a heavier flywheel - a 2 stroke 125 MX machine becomes much easier to ride in the woods (low RPM, partial throttle). With a different chamber, jets, and lightened flywheel - the same machine is good for MX (high RPM, WOT).

In a 4 stroke inline 4 - by altering the length and diameter the individual headers run before they hit a collector will affect the partial throttle performance. Smaller diameter tubes will keep the exhaust velocity higher at part throttle situations, and the shorter the distance to the collector affects the scavenging effect. The harmonics of the exhaust pulses needs to be accounted for as well to limit backfeeding.

Do you think the factory race teams use the same exhuast system for every race at every track? From the outside they may look really similar, but they are custom built for those race conditions based on what the data loggers have reported from testing sessions in similar situations.

Motorcycle manufacturers do not design the bikes for peak performance. They design them to meet the requirements of the government where the bikes will be sold, meet a certain price point for manufacture, deliver a level of reliability, and lastly deliver an acceptable level of performance for the target buyer.