There could be a chance that Idriel, Praetorians, and also the Founder didn't know anything what's happening behind the Eternum (knowing that the Founder can be replaced by the person who collected all the Gems of Doom), Idriel mentioned that The Founder is just a man
By stating this there could be chances that
The Founder also trying to know the what could be the secrets of Eternum (knowing that the Founder could be just a scapegoat stated by Orion before the ending of 0.4). The Praetorians could be also an insider that controls the flow of Eternum and being the Eternum Police and give them the privilege to kill anyone from the game. And why would Idriel say that Calypso is obtainable if She was still not ready from being used? (we all know only the Praetorians said that Calypso isn't ready yet, there could be a reason that they trying to fully control Calypso knowing that Calypso was imprisoned not created) She also stated that she created the Weapon of Atlas and if it's then she could be the one will say that Calypso isn't ready. (also if Calypso was a "Native" of Eternum there is a chance Idriel is lying about creating Calypso I mean how would she create Calypso if Calypso is a "native"? Is she her Mother or something. Yeah... but we could also say that she was created from a code or some shit)
My theory is
someone is manipulating Eternum from behind that Idriel didn't know, The Founder didn't know, The Praetorians...(maybe they know). There's also a small chance that knowing that Eternum is somehow connected to OIAL there is a chance that "inroth" are the one behind the killing and converting dead people to NPC (knowing that Astaroth's objective is to become a God) and they were also hinted that they are still a part of the game as being almost mentioned and ...
being in a "FUCKING NEWSPAPER" and not just a newspaper but not just a normal newspaper it a newspaper from Eternum which is from the game I mean if they exist in real life (from stating that there is a cult and a group named Son of... a bitch? jk "Astaroth") what is the reason behind being in the ingame(newspaper) and real life are they trying to do something or they could be behind all of the reason of the weird things happening to Eternum we didn't know.(and we didn't see death scene of Astaroth soo... maybe his still alive?)
Lets see. About the Founder being "just a man"... well, clearly he doesnt look like it. The Praetorians are under his control as he said at the end of 0.4, and he has info that players have not (like the weapons you found, or the ones related to you). He looks inaccessible in the "real" world so MAYBE he is an AI or for some reason he cant be found (in our world).
So its hard to say he doesnt know whats happening behind Eternum. I can believe that Idriel doesnt know, because she didnt say anithing after your party hacked they way into Ogigia, or after you found Calypso or had a Gem of Doom (the first one). She knew about the second one for obvious reasons (someone "lost it" and at the same time she had to givo you an invitation to you). So, its hard to say how much she know or doesnt know but at least Ill give her the benefit of the doubt in some info.
About Calypso being "not ready", its hard to say. I think that if there are 3 weapons of Atlas, even if they are not ready its something you need to tell to players, even when in your plans you want to control the third one (Calypso) to give it to players or something. A possibility here is that they were trying to give it to Thanatos only, because how he entered Ogigia but couldnt leave? there is a chance that he isnt a hacker and he was able to enter becase Founder, Idriel, or Praetorinas allowed it, but after they were killed he was left there without a way to leave.
Another theory could be they wanted to convert Calypso to a weapon form so it would be "used" in the way they want without her causing problems at will (she knows too much maybe). Remember the Syndicate said she was the key to open the doors of Acheron. This is why I think the Immortals (lets say Founder and others) wanted access to that place but for some reason they cant open it, so, if Calypso is a key, and the gems another one, if Calypso is a weapon and they can cantrol de player that uses it and the one that has the gems maybe the will win what the want there and the player wins something in our wolrd? This makes some sense when you think about Thanatos always finding the gems wherever they are, and maybe why he is immortal too.
About "creating" Calypso, maybe Idriel meaning of that word is about converting here into some kind of weapon, like when you prepare someone for a specific destiny. Or maybe it was a lie, it isnt hard to belive the will lie to us hahaha.
About the newspaper, remember that it was a game event. So he found info about the event like the npc or the pictures or the phone call. Its like every game that lefts info for you to understand context, nothing more.
About the jokes and references to OiaL, well, its like easter eggs, funny hidden jokes or references about other games, like Alien, movies like Ocenas Twelve, or even Gladiator. Its nothing more than a reference or a joke, but Caribdis said that this is the same setting as OiaL but its not a secuel or something strickly related.