I suspect it is mainly due to the relatively heavy flywheel plus balancer shafts needed to give a big twin acceptable smoothness, compared to an inline four. The inertia of all that rotating mass is going to make it harder for the rear wheel and transmission to force engine revs to match road speed, which is what has to happen if you don't use the clutch to allow engine speed to change independently. The GSAP system simply uses electronics to try to mitigate the extra mechanical stress imposed by clutchless changes, but it can't eliminate it entirely.
I still feel that quickshifters generally are a bodge, and while gaining a few milliseconds per change on the racetrack, are not something that road riders with mechanical sympathy for their machine would want to use very often. I recently changed to an RS and deliberately omitted the quickshifter from an otherwise fully optioned bike, after having had GSAP on my two previous GS models. Both of these had gear changes which were quite clunky and obstructive, particularly in the lower ratios, though the later 1250 GS was slightly better. Both also had annoying problems finding neutral which I suspect is due to the GSAP widget interposed between lever and gearbox.
Maybe it is just coincidence, but the result on the new RS seems to be a much lighter and more direct feel to the shift lever, and very nice changes indeed - the best by far I have had on a boxer engined bike. It is also very easy to find neutral.
) then a QS will have some benefits. But "bang bang bang" kind of says it all. Note to self: don't buy a secondhand bike from this man! 
