So has anyone gone back and attempted to use the ATO function on Lythium? So far the helos are popping up in the wrong spots and getting destroyed, Aircraft are refusing to use the runway and troops (as previously mentioned) are extremely inconsistent in their ability to function outside of vehicles.

The Southern airbase has to be "fixed" by the mapmakers. The defined (as the AI travels) taxiways don't match up with the physical/in game tarmac. An easy fix would be to remove the concrete barriers along the way, as the aircraft will move over the grass/dirt OK, but they get hung up for a while on the barriers and either eventually power over or crash n burn.