The Primordial One is a Clone of the Twins
So Melanta said that all Teyvatians are descended from the First Ancestor. Thus those who are descended from the First Ancestor are Children of Humanity-- while the Traveler, who is not a descendant of this ancestor -- is not. He goes on to mention the myth of the Primordial Human: a body created by the God of Light, and stolen away by the King of Darkness. And so the Primordial Human became capable of both great good and evil.
I interpret this to be Teyvat's version of the Fall of Humanity. Not a literal retelling of history, but with some truth still in the seams. The God of Light (Phanes = "To bring light") created the Primordial Human (the first man) in his image. But when the King of Darkness (Forbidden Knowledge? Some other temptation?) spirited the first man away, the Primordial Human was infested by the power of darkness. Thus the Primordial Human and all its descendants came to possess the power of Light and Dark.
But Melanta says that Asmoday might have taken our sibling BECAUSE of something to do with the Primordial Human myth. So even though the myth might not be a perfect retelling, there is something about it (in connection to the Twins) that made her take our sibling. So I started looking into connections between the Twins and the Primordial Human. And I think I found one.
We are not a Child of Humanity, but they are very similar to Teyvatians. In Albedo's first Story Quest, he tests the Traveler's body and finds that we are very much like a regular human from Teyvat. How can we be so similar to Teyvatians, when we are neither descendants of the Primordial Human, nor from Teyvat? Skirk shows that humanoids can evolve on different planets, but even she is distinct because of her Abyssal Affinity and aquatic fins. Since Albedo is a product of the Primordial Human Project, and a skilled alchemist, I think he would be able to identify any outstanding biological differences between Teyvatians and the Traveler, if there were any. But by his own testimony, there aren't. So we're aliens, and yet we're "the same" as the locals? How?
The similarities don't stop at the Children of Humanity. Teyvatians did not evolve naturally, they were created by the Primordial One in THEIR own image. But if the Twins mirror Teyvatians, and the Teyvatians mirror the Primordial One, does this not hint that the Twins are "the same" as the Primordial One, in some manner of speaking? With what we know about the Primordial One's nature, don't THEY seem familiar?
Phanes is a winged androgynous being, who wears a crown and was born from an egg. A Descender, with the will to rival the world, and the means to terraform a planet. If the Primordial Human is any indication-- this entity is humanoid. Meanwhile, the Twins are winged, androgynous-looking humanoids, who are crowned heirs, extremely willful, and in possession of a Pioneer Ship that can terraform a planet. But Phanes was born from an egg, while the Twins were born from a mother (Aether is the older twin, meaning he came out of their mother first). So just like with the Teyvatians, the Twins and the Primordial One are similar-- yet alien to each other in origin. How can that be?
My idea is that they aren't alien to each other.
We know that the Twins were once the heirs of their lost civilization (lets call them the "Pioneers"). But with their world's destruction, they fled on an advanced Pioneer Ship which could terraform a suitable planet into a new home. But with such advanced technology, and faced with the destruction of their world, I don't think it's far-fetched to say the Pioneers might have made more than one of these ships for redundancy.
There are hints of another such ship existing. Before Sun and Moon & Moonlit Offering's Parting Light describe an "Ark" which arrived on Teyvat with the Primordial One. Looking back at the Pioneer Ship's tech (like a gene vault), it would be entirely apt to describe such a vessel as an "Ark". And I think that's exactly what this Ark is: a Pioneer Ship. One that arrived in Teyvat and stayed (it is said to have been "moored" on Teyvat), unlike the Twins' ship, which fled immediately.
It was generally thought that the Ark (if it was literally existent) was a vessel that Phanes brought to start fresh on a new world. But if the Ark is a pioneer ship, I think the Primordial One might instead have been its passenger-- the same way the Twins' were flown around the universe by their ship's AI. So perhaps, Phanes is a member of the Pioneer Civilization, who escaped on a ship, just like the Twins? It seems so. But factoring in THEIR supposed origin from an "egg", I think there's more to it. This is where I go into deeper speculation.
In Gnosticism, the Demiurge is a false god, ruling a false world, who is ignorant of the true god, created by the Aeon Sophia. This false god is a distorted imitation of the true god, believing itself to be the only god there is. It has been widely accepted in Genshin Lore that Phanes is our Demiurge. But if THEY are the Demiurge, then who is Genshin's Sophia, and who is Genshin's original god?
The Ark would have arrived in the skies of Teyvat over 6000 years ago, at the time of the dragon age. Teyvat was perfect for terraforming, but the presence of the seven sovereigns made it impossible to proceed. The Ark's AI (our "Sophia") knew that taking Teyvat would require a conquest it was not equipped for. So in response, I think the AI created a solution-- or rather, incubated one. With its genetic vault (the "egg"), the Ark created a being in the image of the Crowned Heirs. This imitation had everything that the Twins had. Their wings, their appearance, and even their powers-- all necessary to defeat the dragons. But because this being was born in isolation, it believed itself to be the one and only of its kind, the true heir to the throne of the Pioneers. And so it declared itself as the Great Ruler of the Firmament: The Primordial One. With that, it harnessed the powers of The Ark (Celestia maybe??) to change the face of Teyvat.
Things proceeded swimmingly, until the War of Funerary Flame greatly damaged the Ark's systems. So the Primordial One, having lost a critical vessel of power, needed to find a replacement. The Gnoses and the Dragon Authorities fulfilled this role. At some point after the War of Funerary Flame, the Twins' spaceship passed by, and our sibling disembarked.
I'm hesitant to include our Sibling's timeline, since it hasn't been objectively laid out yet. But from what's implied, our Sibling landed in Teyvat alone. when she was captured by Asmoday, then imprisoned in the Temple of Space.
Around 500 years ago, the Khaenri'ahns fished our Sibling out of the Temple, leading to him/her losing all memories. Though they eventually regain their memories, they fail to locate us, because the Traveler is still on the ship.
At the time of the cataclysm, the spaceship landed back on Teyvat, leading to the Sibling attempting to escape with the Traveler. This was followed by our failed escape attempt, leading to us getting captured by Asmoday. But it seems that, after this event, Asmoday vanished-- having sided with the Sibling. I think Asmoday might have noticed how similar we are to Phanes, leading to the eventual discovery that the Twins are the rightful heirs of Teyvat. I think another Shade helped uncover this fact-- specifically Naberius, since she is highly knowledgeable about humanoid biology, as the creator of all Teyvatians.
But evidently, Asmoday left and Naberius got her heart ripped out. I think the Primordial One might have found out about Asmoday and Naberius' little discovery. So THEY ripped her heart out and sealed it in a dungeon, so that no one could awaken the Shade of Life and discover the truth. Simultaneously, he seized the Twins' spaceship to try and force its submission-- leading to the vessel's data being corrupted. But since the ship refused to submit, he instead chucked it to the Frost Moon (and maybe used Irminsul to modify records of its existence).
The Primordial One then entered cryosleep on the Ark, having been severely weakened again by the cataclysm. But unbeknownst to THEM in THEIR slumber, Asmoday has freed the Twins. As for the Ship's AI, the Traveler did not really seem to look for it in the ship when they went to the moon with Columbina. Maybe because they don't know it exists. Or maybe because Traveler already knows where it is. And it, or rather she, has been following us all throughout our journey.
....maybe.
edit: adjusted the latter parts for some more clarity