The Pokémon sent to the PC perceive it as an entire world filled with only Pokémon and no humans, and because so many of them are on the brink of fainting before they get there they don’t remember getting caught, and if you never take them out of the PC they’ll just continue their lives believing they’re still in the wild.
Inside they develop a civilization, have their own economy, develop tools and food not present in the human world, and when they explore the world they find out it never stays the same because the PC loads different floors… I mean, landscapes, every time they visit the same place.
Or if you think about it they’re basically in the Digiverse
But quick balls catch them at full heath and they’re easily the fastest way to catch Pokemon.
Besides, they all go to Pelago now.
Look, I don’t got all the details figured out guys, it’s just such a… a perplexing vault? a cryptic repository? a baffling enclosure? an enigmatic prison?