lakewood – I should have mentioned that I haven’t learned it that Gemara on the inside, I heard it brought up in a shiur so I can’t say that I know if the mefarshim take it at face value but let’s assume they do for argument’s sake. Unfortunately I’m not holding on the level that I can personally offer you any answers that don’t seem somewhat like a cop-out (perhaps there are brighter people than I in the CR who can). But if we observe a natural phenomena which seems relatively predictable yet Chazal states it’s based on human independent human behavior, than what are we really left with other than to say we don’t understand it properly ourselves?
I suppose one could answer that when Hashem designed the trajectory and orbital patterns of the universe and our solar system in general He already knew all of human history so He knew what human actions would merit what astronomical events. You could argue that it would seemingly negate free-will but the whole bechirah/yediah thing is one of the essential stiras of Torah so I guess you’d have much bigger things to worry about.
I once heard in a shiur from Rav Tzvi Aryeh Rosenfeld in which he discussed that if a niddah looks into a mirror that nobody has ever used before then it will get a blood spot on it (if I remember the details correctly). He said that we have to have emunah shleima in such a thing and if we fail to observe the phenomenon occurring then we must assume it’s because on the level we’re holding at we’re not zoche.