How does Riot decide what deals physical or magic damage?

Because the inconsistency is driving me nuts. I play a lot of physical champs and they have random magic damage in their kits for no reason. Like Jax. He jumps to a target (Q) and deals physical damage but then he hits them extra hard (W) and it is magic...? Yasuo as well. Slices you with his sword to deal physical damage but if he dashes it is magic for some reason. But him lifting and suspending you in air isn't magic... And Lee Sin. He shoots a compressed sound wave at you (Q) for physical damage but if he smacks the ground to send out another sound wave (E) it is magic. Last example is Jayce. If he swings his hammer in a downward motion (Q) it is physical damage but if he swings it in horizontally (E) it is magic.

These things make about as much sense to me as making Malzahar's silence deal physical damage or Kennen's Lighing Rush physical. Seemingly random for no reason.