I read that in order to stop the raging beasts the ancient people created the orbs after the legends went to sleep. I think it may be in RSE. If so then the orbs are probably the manifestation of the Power that was taken from them. It'll explain why the beast react to them. On the official site it said they wanted more power for themselves so they clashed. Perhaps that's why they reacted to the opposite colored orb in R/S, they wanted that power. It also explains why having the orbs in HGSS summons them, it's probably similar to how the opposite Lati attacked in HGSS in order to get the Soul Dew. In other words they want their power back, and that of the legendary too...
I like this. There are many things to consider.
At least in Emerald, the legend does not mention where the Orbs came from. If they were created by the ancient people, I think they would have to be containers for their power, rather than manifestations of it.
In Ruby and Sapphire, I remember that both Orbs do something to the legendary Pokémon. One of them (the one the version's team steals) awakens it, and the other does something else. Remember that we obtain the Orb that our version's team doesn't steal and then it shines when we approach the legendary Pokémon; it is after that happens that it battles us. I don't remember (if it is stated) what our Orb does to it.
And who knows, in Emerald the Orbs may have become inert after Team Aqua and Magma used them. After Rayquaza stops Groudon and Kyogre's fight, the legend told at Mt. Pyre changes to mention that Rayquaza stopped the battle, but the Orbs are no longer mentioned. Also, they are not required to battle Groudon or Kyogre when we find them later in their caves. It may be that the Orbs only contained the power that Groudon and Kyogre needed to reawaken, and if so, their Primal Reversion may have to be triggered by some other object.
The official site mentions that they got their Primal forms by absorbing nature's energy, and that in the time when they first transformed, the world was overflowing with that energy. Maybe in the present day nature's energy is not as strong, and what they need to achieve Primal Reversion is something that helps them gather enough of nature's energy from around them to temporarily activate it.