I am no expert, but have read some about exhausts in different applications. It all comes down to how well the 2 into 1 system is designed. I got the following from
Dennis Kirk:
"With 2 into 1 exhaust systems, the two exhaust pipes combine to emit fumes through one muffler. Sound will obviously vary depending on the pipes and muffler, but these systems are generally characterized as being higher pitched compared to true duals. These pipes are also typically lighter, meaning you can shed a couple pounds off your bike, especially if you buy pipes made with lighter materials like carbon fiber and aluminum. They generally perform the best at low RPMs, which is where most riders will notice an increase in performance. With that, though, a 2 into 1 system may hinder top end performance.
"This design also aids in one other special advantage, a benefit referred to as scavenging. When the first cylinder sends a pulse of exhaust shooting down the pipe, it helps to pull oxygen into the second cylinder. Then, the second cylinder helps the first in the same way, and the cycle goes on. 2 into 1 exhausts can offer a better balanced airflow in your engine which can result in more torque and a smoother idle."
As I recall the scavenging is dependent upon the pulses of exhaust from the two cylinders doing a nice zipper merge at the conjunction of the pipes. The timing of that is determined by the lengths of the header pipes. Get the lengths wrong and you have exhaust from both cylinders hitting the junction at the same time and it chokes.