Maybe a solution to this could be to limit the collision detection boxes only to those trees with some likelihood of an aircraft collision.
The whole map may have hundreds of thousands of trees, but most missions only have aircraft over a small portion of this - usually in fact a very limited area. Activate the collision detection within say a 5 or 10 mile radius of where the planes actually are and ONLY if they are below a certain altitude.
It would be similar to the way the lod switching is done - only it would have to track all aircraft not just the player's.
I raised this idea before and it still seems like a good solution to me. But it is also true that I know absolutely nothing about game development, so it may not be technically feasible for some reason or another?