Here is the ignition maps for the Aprilia and the xt660 for comparison.

The first one is the XT660 ignition map.



And this is the Aprilia ignition map.



As you can see the ignition timing on the XT660 is way diffrent on the area were most of us feel the surging. Around 3000 rpm area or the cruising rpm. And on WOT the diffrence is minimal.

There is also a big difference on what RPMs the changes are set. As you can see in the pictures Yamaha and Aprilia has chosen diffrent throttle openings to tune and compensate.

It could be that the yamaha was made for more markets in the world with diffrent demands for the combustion regulations. And because of that had to make changes that will affect the performance.
Aprilia on the other hand has less markets and sold mostly in contries with high quality fuel.