We did a survey of 3rd Gen bikes, and in every case the white painted screw was the one that was left fully closed by the factory. Recreating fully closed is pretty damn easy, if you ask me. There is no magic, or ECU requirements going on here.
Minimizing the bypass air through these air screw passages became important in 3rd Gens when Fly by wire was introduced. With that change, the cold start high idle mechanism and the warm idle speed adjustment screw were eliminated. All idle speed (both cold and warm) is now a function of the ECU opening the main throttle plates more or less to achieve the required cold or warm idle speed. So minimizing leakage air around them means the throttle plates will be open more at warm idle and allow it to regulate properly.
There have been some instances where people have found, over time, that one or more of the other throttle bores had lower vacuum than the reference even when that screw was also fully seated. In that case, the one with the lowest vacuum when they are all fully seated becomes the new reference, and you just open the other three to match it.
One more point: If you still have increased vibration after balancing the vacuums, I would suspect the instrument you are using to balance them. Once you have it well balanced, try swapping vacuum hoses around. 1-2, 2-3, 3-4, etc. If that changes any of the balanced readings then the gauge is your problem.
