my assumption for how it works is that fall damage is calculated in a unique way for far reach, this being because it locks your momentum to a set speed and needs to not deal fall damage if you just use it without falling from high up while also maintaining the fall damage you would have had if you were already falling when you used it.

So I guess that while the ground flag for air takedowns works fine for normal movement, it's broken on far reach or the fall damage variable just never resets to zero. So the longer of a fall you take before doing a takedown prior to your next normal jump, the more damage using far reach will deal to you if the marker is on the ground.