Hey! You asumption that change the Pokémon by day can't be done isn't really accurate.
You see, the system checks the "time of the day" to change the palletes, is just changing the wild Pokémon instead of the palletes. It's just an effect change, with the same condition. It may be related with both D/N system (wich checks the clock), and the [email protected] system, the only wild Pokémon data changer in-game I know.