I'm just gonna keep adding to my own wild theories here for anyone interested.
Replaying the game, Caribdis hides so much in the tiny instances that I'm only just finding. The chapter-ends with the flashes for MC hide a lot each time (0.1 shows Benjamin, Thanatos, Idriel, the Founder, and an Ion Praetorian with different eyes, or at least I think they look different, 0.2 shows some sort of weird russian basement wherein MC meets his doppelganger then there's like a tornado of blood and the doppelganger is gone? Will update as the playthrough gleans more).
Also, went on a weird tangent to look into a bunch of the Greek mythology that's Caribdis has used. The obvious being Calypso stuck in the Ogygia server by Ulysses (the Roman, and thus B*stardized, version of Odysseus), reverse of the greek myth. Each of the weapons of Atlas share a name with a greek titan's child (Specifically the Oceanids and Atlas), Hyas being a hunter, Dhione an oracle, and Calypso a sorceress, meaning Nova's comment that Calypso could be magical since Hyas is melee and Dhione ranged isn't crazy.
Spoilers for 0.6, Thanatos has Hyas.
Hyas' only achievement was getting killed while hunting lions, so I think we may see Thanatos hunt the MC and his harem only to be killed by his own prey. Dhione being an oracle, a being known for foresight and prophecy I think fits well with Nova, she's the obvious nerd-brain of the crew (They're all smart though, which honestly makes all of them best girl imo) with her eye being both a strength and weakness for her. Calypso's connections other than being magical and trapped I've drawn a blank. Random connection though, Calypso's blue flash being released is the same coloration as when Eternum connects to the MC, which is probably to do with Calypso's portal ability (possibly her ability being what allowed Ulysses to create the Exit Portals and connections to other worlds?) and trapping her in the box whilst having similar boxes be what frees NPCs from Ulysses' control makes her the crux of whatever is actually going on in Caribdis' story they're expertly weaving.
Again, will probably post again tomorrow as I go frame by frame through other sections...