The only shortcut I can think of (without being much of a server expert and based on my experience) is to completely remove the wild pokémon and manually place them in the overworld and nedert through pixelmon spawns the way you want....
Surely there are other more efficient ways, most likely if you have your own server you can give each world or dimension its own configuration and interconnect them with the rest.
Good luck with your project.
{
"tag": "gen5",
"dimensions": [
72
]
}
Alternatively, you'd have to activate the External Spawning JSONs and add a "dimensions" condition to each Pokémon, with the respective ID of the dimension you want them to spawn in.