So... what are Groudon and Kyogre then? Just some random Legendary Pokemon that was found which just so happened to have powers matching that of "Groudon" & "Kyogre"? And it also just so happens that the Orbs which were used to "Groudon" and "Kyogre" work in a similar way to these two Legendary Pokemon? And that, despite never having fought each other, once they break loose of the villain team's control they for some reason both went to the same place and started fighting with one another like "Groudon" and "Kyogre" did? AND then there's this third Legendary which just so happens to fit the description of "Rayquaza" which can also be summoned like it to also go to the same spot and just so happen to have the same ability to cause these two Pokemon from fighting?
I think you might have it a bit reversed. Groudon and Kyogre were likely discovered first, and so were the orbs associated with them, before any myths were created about them. The likely situation is that the people of ancient Hoenn discovered these two super powerful, extraordinary Pokemon who have the power to cause droughts or heavy downpours as well as two powerful orbs that are used to awaken or control their power, and the ancient people of Hoenn were in complete awe of how extraordinarily powerful they truly were, likely having witnessed said power at some point as well. In such awe and admiration of how truly powerful they were, the people created myths and legends about these two powerful Pokemon and attributed it to them in such reverence of their awesome power and essentially began to see them as deities, even naming them as "creators" of the Hoenn region and creating a story about them in doing so. The same likely goes with Rayquaza too: they discovered its existence at one point, and also further attributed some stories to it in reverence at witnessing such extraordinary appearance and power that Rayquaza has. As time passed, the myths and legends the ancient people of Hoenn created about these super powerful Pokemon were passed down over time, possibly being changed somewhat over different retellings of said myths over the eras.
It's not so much that Groudon and Kyogre's myths were created first in other words: it's that the actual Pokemon themselves were at one point discovered, if not outright seen by ancient people and people witnessed these ultra powerful Pokemon and gave them stories and myths because they had so much reverence and awe in beholding just how powerful they were. Power in the eyes of the beholder, and the beholder creates a story to revere and possibly emphasize just how strong these extraordinary Pokemon really are.
It's like how Dialga, Palkia, and Giratina likely do have powers over time, space, and antimatter, but the myths exaggerate them greatly and ancient Sinnohan folk created stories about them (and the Lake Trio+Arceus) after they beheld such awesome power from these Pokemon. Giratina likewise definitely has exaggerated myths, like how some consider it "banished" and "exiled" and attribute it to being an evil being, but its portrayal in Platinum shows that it is, in truth, a chaotic neutral being that simply lives in a world where the laws of matter and physics are reversed, and its existence vital in that it sustains the real Pokemon world, but it's not truly malevolent, and it's very protective of its home.
Many other legendaries such as Lugia/Ho-Oh, Raikou/Entei/Suicune, Reshiram/Zekrom/Kyurem, and Xerneas/Yveltal/Zygarde likely also have this nature: rare, extraordinary Pokemon that have unique and extraordinary power, but any stories associated with them are very much exaggerated or myth. Notably, the latter group with Xerneas, Yveltal, and Zygarde are pretty much the most mysterious group of "major legendaries" and not much is really said about them, really emphasizing that they are elusive and magnificent, and it's likely in that case that those three were the most elusive even to people of ancient times.
Essentially, many of these legendaries have extraordinary powers, but the stories about them are "created" by people of ancient times who beheld their power with their own eyes, but created stories because they revered these Pokemon's awesome power so much.
That's sort of the idea, I think.
