>>44263263I like to just explain it with an unseen force/psychic types/Never seen before legendary/whatever bullshit. The rooms are kept into a sort of stasis and the pokemons there are disconnected/got used to live into the dungeon. It's a simple answer for the gimmick, and makes the world a more curious place to live in
The world is already wide as fuck, so the in-between and travel to that mystery dungeon should shine more than the mystery dungeon itself