Gamefreak game design meeting
>You know it would be cool if we added all the bad team leaders to one team.
>Sure, we'll use the original designs to clearly reference the various games.
>Sounds good, let's do it.
How underaged retards think these meeting goes
>Hey, let's add the evil team leaders from previous games.
>Yes, they're clearly from an alternate universe where x and y and z.
The alternate universe stuff is just a lazy way of letting them do whatever the fuck they want. Judging by every pokémon game I have played, it's crystal clear that they just added this without any thoughts to whether or not the designs make sense in-universe.