You've done an excellent job of calling out a lot of the thoughts in the episode, and I'm gonna try not to dig into those too much. Mostly, I'm gonna put out some of my thoughts around a few items and the series in general. Also, a caveat, I haven't done the true ending, and I ended up avoiding the reset when picking between Aldo and Mariel, so I don't have the whole story.
This is, frankly, the heaviest story we've gotten out of Another Eden yet. Sure, some have pushed the boundary on philosophy and identity, but they've implied most of the darker elements. Here, they are front and centre. I think of this episode a lot like I think about literature and analysis. There's so many ways to read things, and so many perspectives on how to read it, you'll find a bunch to chew on (#notSorry).
All that said, I found it to be very biblical in nature. There's salt pillars, parables, Christian communion, Garden of Eden (location and the pursuit of food/knowledge), saviour sacrifice, and so much more. Then it layers in psychological elements with Marie and it gets very interesting to see all these parts come together.
What does stand out to me, at least as far as the other episodes are concerned, is the amount of self-reference. The other episodes connect to the larger AE story because of their central character (even in Road to Thunder with the fangirling by Miyu, and Fatum with Alma and Lele's friendship). Babylon stands out for two reasons, though: there's a TON of references to other bits of AE lore (clock tower, Ivan/Phantom, guardians, etc) and the lack of connection between Marie and Mariel. Marie isn't explicity Mariel, isn't from the same time period (maybe; see below), and Marie isn't explicitly a religious figure like Mariel. Mariel doesn't fulfill the central connection we've seen from the previous four episodes, and I think that may be telling.
Again, even though I don't have all the details, I'm gonna go out on a limb - and probably fall flat as a result.
So, what could it be telling us? Time for some head canon: What if Marie isn't Mariel? There's nothing in the story, that I saw, that actually connects them. The story even implies a break since the story they both relate is different. They have different experiences. All of the Vortex stories until this point have been historical; they lead up to the modern world of AE. If that's the case, this story shouldn't be about a parallel Mariel. So who is it? I think we get a hint on that, as well. Those references to the Guardians and Tower are intentional, as is the state of the modern map: Babylon is Zerberiya, the religion is the Sword-wielding Savior, and Marie is Thillelille. Basically, between Antiquity and Modern there's been a massive collapse in Zerberiya (not surprising based on what we know) and so over generations there has been decline. Thillelille is actually the reborn Sword-weilding Savior, maybe even born yet again, and the sword Ivan leaves directs us that way.
niantre