Ground feature echo (mentioned in the article)... possible. Not mentioned here or in the article: thermocline in the atmosphere. Thermocline in the water is traditionally how submarines "hide" from surface ships.

I hear flanging from the planes incoming from quite a distance, and they're pretty low when the fly over where I live. More telling: I can hear the freeway and the busy arterial, "depending on how the wind blows". Sometimes it flanges, too.

So: ground reflection along with thermocline refraction seems a perfectly plausible explanation for one source of the phenomenon; could be several, probably all involving ground and atmospheric factors.