The SE RNG is weird, but these massive differences in drop rates shouldn't be possible even with this. It can't be coincidence and there must be some kind of system behind it.
It's more likely that each atma can have a different drop rate and nobody has figured out the system behind it yet. I think that all players that farm for atmas in just one area for hours are doing it wrong. So the best option for now seems to be to change areas frequently.