The #1 cylinder usually gets robbed of air since the other three cylinders are positioned before it and the stock plenum's shape doesn't help for the air flow. The skunk 2 and other aftermarket manifolds have solved this by the shape of the plenum to ensure that all cylinders get all the air they need by using the physics of the wave you are describing.

And about the butterflies. The air is bypassed to the long runners running along the top of the manifold before activated by vtec. Then, when activated, the short runners and the longer ones used before are both open for air to pass through. The short runners acheive high power under high RPMs and the longer runners acheive "high" torque under low RPMs.