What do you mean, I'm not sure I follow? Balancing the rotating assembly removes many of the small vibrations caused by removing the balance shafts.
As I understand it, balancing a rotating assembly is much like balancing a wheel, thought instead of putting more counterweights on it, the components are progressily shaved until they reach as little 'wobble' as possible.
Balancing a rotating assembly is simply that, balancing the parts that comprise the rotating assembly.
As you could imagine it would be hard to get the counterweights cast perfectly each time on the stock crankshaft from factory (well it's further than what the manufacturer is willing to go/pay, and is not really neccessary for stock standard cars).
Balancing the rotating assembly is basically to perfect the 'rough' weighting that is innate in the cast item.
Balance shafts were introduced to overcome a seperate vibration caused simply by the operation of an inline engine. The horizontally opposed Subaru engine does not have this problem, simply due to it's configuration, it's a flat four engine, not and inline four. It is not only Mitsubishi who tried using balance shafts in the inline engines, Mitsubishi only coined the name 'Silent Shaft'.
Dude, read the link in the first post, this is an extract from it - "Balance shafts are commonly found in inline four cylinder engines such as the Mitsubishi 4G63 which, due to the asymmetry of their design, have an inherent second order vibration (vibrating at twice the engine RPM) which, contrary to popular belief, cannot be eliminated no matter how well the internal components are balanced."