I just noticed something. Notice how they both appear in the water. Perhaps this is the fight from Emerald? It would make sense given how HeartGold and SoulSilver added in some elements from Crystal. Also, it's definitely not the Cave of Origin encounter, and if they wanted to show scenes of them being sent out by a trainer, they could be sent out anywhere, and it would make more sense to show Groudon on land. They specifically showed them both appearing in the water. Something to ponder.