In recent game worlds, it does seem like the flight interval calculator (or whatever you want to call it) is beyond drunk. The penalty, as you say, should be on a linear scale, and you allude to the fact that it should not be a hard penalty in a previous post. Yet, in previous games I ran 40 minute separation on 2200 pax/day routes with no problem but in GW1, for example, I am seeing signs of overlapping flights on JFK-MCO, for example, at about 2200-2400pax/day. In GW2, similar routes from SHA (CAN, for example) seem to be operating just fine at 40 minute separation at about 1900 pax/day.
Maybe an update to the flight separation rule is in order? make the penalty on a scale like the too small penalty, where "just a little" too close brings, say, a 10% penalty and if flights are more than 20% over the separation limit get the full penalty? As mentioned in other threads, if changes are made, the separation limit should take into account suitable departure/arrival options and lower the departure intervals accordingly. For example, JFK-LHR departures are limited to a few hours in the morning and a few in the evening making it virtually impossible to serve the full demand on this route even with "proper" iarcraft.