The story for Pandora at AK is that it is years (about a century) after the movie has happened and now humans are working with the Na'vi in order to fix the damage that was caused during the movie, now there is ACE (Alpha Centauri Expeditions) to take humans to Pandora. So, for example, outside of Pongu Pongu there is the AMP (Amplified Mobility Platform, basically a mech weapon featured in the film) that was abandoned and left behind. The Na'vi are still there, hence, the Shaman of Songs in the RJ ride. That ride is to connect people to the world of Pandora in the sense that it lets you see how everything fits together and shows off the beauty of Pandora when we don't "fight against it."