That is true but on the inlet side the aim is to get the last possible positive pressure wave at the back of the valve, just before the inlet valve closes. That way the refracted negative wave can not come out of the cylinder.
The main use of the higher harmonic orders is to slightly improve on vol-eff at lower speeds which is why production cars have longer manifolds, this means that you will have less of a speed range between each tuned harmonic. What I mean by using these multiple harmonics is not using multiple harmonics at each induction event but rather, the tuning length chosen means that the positive wave gets back just before the inlet valve closes at more than a single engine speed but the amplitude of the this wave is less as the harmonic order goes up.
The traveling waves going up and down the manifold at higher inlet to cylinder pressure differences have small effects on cylinder filling so they are neglected except in the cases of theoretical/academic work. What really matters is the inlet pressure when the flow through the valves is just starting to reverse.
Another interesting point to note is the pressure waves do not take the same time to travel up the inlet as they do down and it isn't simply a ratio of the main air-stream velocities.