The Anime, Manga, and Games are all completely separate continuities, though. By the time Agatha appears in Pokespecial, the manga went pretty off the rails from the games, the quote of Satoshi Tajiri saying the manga was the closest to his vision of how the Pokemon world worked was made really really early on in the series' life, before it got very different from the games(which happened sooner than most realize), and the fiddly details of both the anime and the manga don't need complete input from Game Freak.
You can pretty much disregard any backstory details from one continuity for a character in any other.