This has been a sticking point with me as well, and there's some solutions that I was going to try using.
First, when playing on a decided non-urban area with clear terrain, replace the At the Deck rule for aircraft with: Nap of Earth, which is mostly the same as At the Deck except if the 2d6 roll is failed (rolled a 2) then the aircraft loses 1 damage points instead of immediately crashing and dying. This represents flying in more open countryside with relatively softer things to collide with, instead of tall urban areas with tall lights, signs, bridges, etc.
Flying at the deck causes aircraft to count as being 2" above the ground, which is easy enough to have a 2" high hill, or large trees block LoS.
You can also try making some thick forests count as a kind of structure that infantry can garrison.
But overall, yes, there are some issues with the rules in terms of terrain neutrality.