If I understood you correctly, are you saying that the mass is more centralized side to side in a V engine?
Can you elaborate on the balance shaft?
Basically, yes. Because and inline 4 engine is wider, it may require more force to rotate it around its vertical axis, all other things being equal. For an extreme example, try spinning a pole vs. spinning a block of wood of the same mass. It's much easier to spin the block. Again, this would all be dependent on the actual dimensions of each particular engine and bike. Obviously, Aprilia is satisfied that their V-4 design has an acceptable moment of inertia and center of gravity when compared to I-4 designs of similar power. It's definitely something they calculated. I would guess that suspension geometry would have a much greater effect than engine configuration.
Scratch the balance shaft, add "smoother." Most 4-cyl. cars have a counter-rotating balance shaft to cancel the 2nd harmonic. I assumed that bikes did too, but I was wrong. That makes sense when you think about it, since the balance shaft rotates at twice the engine speed. In that case, a 90 deg. V-4 will be smoother than an I-4 because its primary and secondary harmonics are balanced, like a V-8.