I'm loving the lore as well, and there's just so much to unpack! I must've missed the upside-down room--will have to pay closer attention the next time that I'm there!
One thing I forgot to mention in my original post--the mysterious recording on the Library's resonator. The third recording is obviously a pre-incident conversation that serves to explain to the player what the contraption is and how it works. The second recording is the one left by the Old Alchemist. The first recording was left by at least two individuals, although who they are or what they are doing there, or when their visit took place remains a mystery. The scraping of metal on stone and rythmic clicking suggest maybe the Eidolon was active at the time, or perhaps a semi-mechanical entity. It could also refer to a hidden mechanism in the Archive itself.
On a whim I also googled "rubedo" and it seems to be a Latin word meaning "redness", while also referring to the finished work of an alchemist. Continuing with the theory that the Old Alchemist is indeed Jonas Falx, I'm thinking that the mentioned combination of blood and temporal flux was possibly a critical key in whatever took place with the Salvation Engine; either to allow the plan to function in the first place, or bringing about the temporal chaos that exists in the world as we know it. The Alchemist also mentions that "rubedo" applies to more than just blood/turning things to gold; rust just happens to be a red color as well.
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"Aren't you listening? I said there's too many missing. Sure, we were dying like mayflies and mind you, some things are a bit hazy for me towards the end, but even so. They can't have all perished and they can't have all turned. I cannot be the only one. But where are they? That's what it always comes back to."
"No, they hardly know anything. Of course it pains me to see them suffer. They're like... little lost children huddled in their homes. But it's for the best. We had all the knowledge in the world. And worlds beyond! And what good did it do us? No. Best leave them to it. Let them think of me as some mad old sorcerer and leave me in peace."
I'm not sure if the Alchemist is talking to himself during the recording, or someone else, but he does seem to be talking about the seraphs here, at least in the first part, although it could just refer to humans too. Humans do still exist in the world--the traders are still human, after all, and mention the existence of villages. While they are polite, they also treat the player as an "other", mentioning that "more like you" have been appearing out of nowhere of late. As for the "they" in "they can't have all turned", this could refer to either seraphs, or drifters. Seraphs were turned from human, although the how or why isn't really known. The scenes described in "Confession" portray much of humanity's remnant displaying drifter-like behavior, although they seem to treat the author(presumably Falx) with great reverence. Of course, I suppose the Alchemist's second statement could just be describing the current remnants of humanity struggling to survive in the new world.
Another oddity that crossed my mind earlier today in regards to the seraphs--someone had to have known a little about them prior to the player's arrival, given the existence of the tapestries and paintings in-game. From a technical standpoint, they're just items that players can use to decorate, but the tapestries specifically have a definite lore component to them and are described in a different fashion than the flavor text accompanying other items. The tapestries seem to depict greenish-grey humanoids in most cases(seraphs), with dark grey humanoids that seem to be a match for drifters. The same dark grey humanoid also appears in the Rot tapestry. The tapestry descriptions also seem to be written from the perspective of the player character; the scenes depicted carry a certain familiarity with the prior and current realities, but the details are all still fuzzy. There also seems to be a distinct disdain for the nobility, which seems logical for a band of common folk loyal to Falx.
In any case, it does beg the question--who made the tapestries in the first place? Was it other seraphs, who perhaps also built some of the ruins we find scattered around but didn't survive? Was it remnants of humanity, although that seems a bit of a stretch especially given that survivors perhaps hold some animosity towards Falx regarding whatever happened with his plan. It could also just be a bit of a plot hole that may or may not be clarified later on.
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So much to consider, haha. I'm probably going to end up starting another world and giving a different class a whirl, and pick apart the pieces some more. I think I've found most of the current available lore in the game; the only bits that seem to be missing are a couple of tapestries and maybe a scroll or two.