I would guess there aren't "rules" for it because the systems are so complicated - it'd be like flipping a coin and trying to figure out exactly why it landed on heads...

Yeah. Not that people don't try to do it. Occasionally you hear people trying to make arguments from geography or weather patterns, suggesting that certain sound changes are more likely in certain types of areas. Nothing substantial has ever come of it, and I think your coin-toss analogy is apt.