The Engine Pro book on this site (if you don't have it buy it!) has some good examples of formula to illustrate this idea. While it does assume a 2nd harmonic intake length in all cases it does consider for example the effectiveness of plenum resonance in different manifold configurations to partially determine the difference between the duration of the intake and exhaust.A cam designer must now be able to look at cylinder, inlet manifold, inlet port and exhaust port pressures (hugely affected by exhaust system geometry) as well as the PV curve for each cylinder to be able to move the ball up the field.
If the program allowed for different intake lengths, I assume there would be an additional factor for that. I have experimented with adding a factor for ram-tuning effectiveness (determined by the length and wave used) to his formula and when you adjust it to match manifolds other than the 2nd wave optimum stuff in Engine Pro, the cam recommendations match very close with what we see in use for non professional classes. Without those adjustments it is much more like pure racing cam parameters.