1. The Rayquaza and Groudo in the special episode are in the anime for Pokemon ag, which is Pokemon Emerald

2. And then there’s the dwarf’s There is no story or animation, it’s just the big challenge area for clearing the game Emerald

3. It’s the Pokémon upstairs, the animation is Pokémon dp, Pokémon Pearl Diamond version

The above comics are all special chapters

The new anime has Pokemon bw, Pokemon black and white versions.

Animation and comics are completely different anyway