EDIT: There are some more theories here:
https://engineering.stackexchange.com/questions/4238/why-are...
Obviously there may be many contributing factors, but I expect one is dominant. This one is most convincing to me: The flyover ramp generally needs to go over some things and under other things. Additionally, for both safety and rider comfort, the ramp needs to be vertically smooth, not having fast drops or rapid climbs. That means ramp A might pass over ramp B by a lot more than the minimum amount because ramp A also needs to pass over ramp C just a bit later, where it does so by a much lower amount. With many overlapping constraints like this, most ramp intersections are much higher than the minimum clearance even though none can be lowered without either (1) making one of the clearances below minimum or (2) forcing a ramp to rapidly climb/descent.