1: Gamefreak made it that way. Don’t know why they put in that much extra work, but they did.
2: Maybe to differentiate the two games. Gold and Silver were drastically different drom both RBY, and RSE, in a lot of ways. Maybe Gamefreak wanted an incentive to buy either copy, with RBY, save version exclusives, the games were identical. In RSE, the plots were slightly different. In GSC, they decided, hey, let’s change up the sprites so they look different with either copy.
3: (Unlikley one) In Crystal they were moving, and so were a combination of both. Maybe Gamefreak purposely made two different sets to combine the sprites?
Source: Sprite differences: (I’m very, very sorry for all the curse words, Please don’t flag this for that, it’s the best one I could find.) Click Me Please
For The reasons why: My brain