This could be a matter of trying to tweak scavenging somehow. On 4 cylinders, the crossover is more symetric, but with a V twin, they might have done something odd to account for the uneven pulses.
Or it could be their method of quieting the exhaust on one side, to change the exhaust noise level at a certain position behind the bike to meet noise emission requirements.
Do the aftermarket full systems have something similar? IIRC, they were run in Superbike for a year or two, so there probably was some testing done on this.