So, my mind wandered as I was out jogging and I came up with a theory that kind of ballooned into a crazy string of connections. Looking back through the search function I don't think anyone has proposed this before, but I might be wrong. In either case, my crazy theory:
The Lord of the Dark is the Great Lord of the sea-dweller alternate humans.
Here's my logic:
A theory I've seen thrown around is that the Lord of Dark, despite being the one in charge of the Dark trait, is not actually the 7th Apostle but something that took their place. Aglaecwif lists the Lord as something separate from the 12 Apostles when talking about the gods the monsters worship. She also calls the Lord of Dark by the alternate titles of "God Slayer" and "Apostle Devourer", so that raises the possibility that the Lord of Dark has authority over Dark by right of conquest, and killed the actual 7th Apostle to consume their power.
So why the Great Lord of the sea-dwellers as this usurper? Well, for one thing, it just fits his character. The Lord of Dark has declared war against the gods, in the name of severing their parasitic connections to other life and freeing the cosmos from them. The Great Lord of the sea-dwellers fought a war against the gods to prevent them from binding his people in their parasitic connections and making them slaves or worse. Plus, they're both called "Lord". Maybe that's a spurious argument, but it would be odd for a narrative to have two guys called the same thing with the same motivations that have no connection at all.
In terms of more specific connections, we know the Lord of Dark has a dead wife. He says as much to Valravn when turning him into a monster, that he's doing it in memory of his bride. Meanwhile, the Great Queen of the sky-dwellers, the Great Lord's counterpart, appears to have died before their war with the monsters was over. In the memory we see in the second Nyx dream, the sky-dwellers are motivated by sorrow and the Great Lord is fighting on his own. The Great Queen dying would fit that.
On a related note, the memory refers to the sky-dweller warriors as "valkyries". The mythical valkyries, the demigoddesses that took the brave to Valhalla, were accompanied by ravens. So the Lord of Dark selected a raven as his Chosen in memory of his bride, and the Great Queen had warriors whose names evoke a connection to ravens. That feels meaningful, to me. Hell, valravns and valkyries even come from the same cultural background and are etymologically related. The "val-" prefix translates to "of the slain". Valravns are the ravens of the slain, valkyries are the choosers of the slain.
Also, the Vestige spoken to in the dream accompanying Heri up the tower can be asked about Henri, and says this: "His like has not been seen since the time of our people. Of our great lord...If properly wielded, even a god would not hesitate to bring down their full might in opposition. As was the case with our great lord. We are surprised he has been allowed to live. His like have been reviled since our fall." So the great lord was a superhuman of the same incredibly strong sort as Henri, one that the gods themselves had to fight with all their might, and that after the fall of the alt-humans his kind were considered a priority target for elimination. It sounds like something the Great Lord did in that battle made them warry of his sort of being. Something like killing an Apostle and consuming it, perhaps?
Additionally, if you prescribe to the theory that Henri is a dual-spawn and his "lost power of a forgotten god" is an Arbiter trait, that furthers the comparison to the Great Lord, as the alt-humans seem to have had access to an Arbiter trait. Going back to the second Nyx dream, the memory shows that the alt-humans were working on a soul-powered weapon for the Great Lord. Soul is the Arbiter trait composed of Dark and Light. Nyx even says, when activating the soul orb she harvests from the ruins "Heh. The dark, the light, and...". That implies a thesis-antithesis-synthesis relationship and that it is indeed the Soul that's being invoked and not just some other means of manipulating soul energy, like whatever Nyx herself uses.
So, then, to summarize, my theory is that the Lord of Dark originated as particularly powerful superhuman in the sea-dweller civilization. He ascended to the position of their ruler, made peace with the queen of the sky-dwellers, and cemented the union between their peoples with a marriage. Together they led their peoples against the monsters, but she died and he was left to face them on his own. Against the odds he managed to defeat the 7th Apostle, consuming it and taking its power for his own. But his people fell, and now he's waging his war single-handedly.
Or maybe he's something else entirely. But the more I thought about this the weirder it seemed for these things to not be connected, so here's my big scrawling conspiracy wall of a theory. I look forward to people poking at my logic.