When there are no trees you could safely fly under the AI.
Ah. I see. Yeah. Can you tell if you are over ground or over water?
Maybe at least have a optional hard deck value in the Mission Flight properties dialog in the mission editor? If I know 99.9% of my fighting is over land, I'd just put a 100ft buffer in there on the flights. If I'm designing a mission over water, I might set it to sea level. That would allow the mission designer to control.
It is surely weird to watch them constantly flying through tree like ghosts. It really breaks the suspension of disbelief.
[edit]
On second though, the hard deck value should probably be in the segment properties not on the flight. That way it can be left at 0ft for take off and landing segments, but set to 100ft for patrol or attack. Unless those patrol or attack segments are over water and then you can leave it at 0ft.