the idea was mainly for Harley's where one cylinder sits in front of the other and the heat and everything else is badly made and or compromised
on the GS could be any of these I'll put a % at the end as my guess why...
Exhaust length before silencer (5%)
Awful air box design (10%)
Potential airflow issues inside the airbox arguing with each other (10%)
Shocking manufacturing tolerances in general (10%)
Poor tolerances in the actual combustion chamber (5%.... but could be far more)
Ignition spark wandering about vs when its should fire (5%)
Compensating for an appalling ignition map (20%)
Lots of other stuff I haven't thought about or forgotten
Probably exhaust pipe lengths. Akraprovic try to mitigate some of it with expanding cones at different lengths. The 2:1 Y joint probably does more to stifle power than it benefits in saved weight.