But again, this is piling up to the point where while I could be wrong and you could be right, I don't think it's fair of you to be acting as though my idea is foolish or illogical. It has potential points where someone could nitpick; it's not a bulletproof syllogism of perfect deductive insight. But then, neither is any other explanation we can construct at this time.
I want to throw this up to the top, because you and me have a history.
I'm not trying to call you foolish. I'm not trying to attack you for not having a perfect, unassailable argument. I'm not saying my theories are completely without fault.
What I am doing is approaching the assertions, examining them, and trying to make sense of the information in the context of those assertions. People began defending the idea of the Throne being artificially constructed as though it were "Word of God" and I wanted to point out that that was an assumption, potentially an unfounded one. I'm not attacking you. I'm not trying to tear you down and cast you into the mud. I'm examining the evidence, examining people's proposed theories, and seeing where they don't quite match up.
So please, do not take this personally. Because the more riled up and personal you make this, the less actually useful discussion can be had.
The point is, nothing about the place Beryl's currently camping out sounds like a natural place or a part of the balance of the natural order. It's not just that it's lifeless, it's not just that it's in a weird spatiodimensional fuckery zone, it's both.
This place might be natural because nature is sometimes stranger than we imagine. Or it might have once been natural only for Beryl to corrupt it into a weird Hell-zone that she likes because she's the only one fully equipped to understand its weirdodystopian characteristics.
For example, you are assuming the Throne is connected to the spatial dimension that Beryl is in, while I see the text clearly spelling out that the Throne isn't really in that space. The Spatial Dimension Beryl finds herself in does not seem in any way tied to the Throne, they are separate things. Going forward that the Throne must be unnatural, because the spatial dimension Beryl is in is unnatural ignores the metaphysical aspects of Beryl not literally sitting on the Throne.
My proposed theory about the Spatial Dimension Beryl is in is that this is that Selene used the Silver Crystal to suck in Beryl, Metallia and many of the Youma, creating a magical black hole, that we have seen as the hole in space above Selene's hand in the Lunar Palace. We know the Hole is where the Silver Crystal was, and it would fit as the type of act she might take. It would also explain how Beryl and the Shittenou survived Saturn's attack, they were never in the dimensional space to get hit.
But it might also be synthetic, a product of someone's twisted and malevolent designs, either using an old and now destroyed Throne for parts to build it, or creating something entirely artificial to usurp powers not normally available to human(ish) mages like Beryl (was).
I mean, fine, there could be some kind of Throne of Rock Anima that in the Silver Millennium was occupied by some rock-monster guy or something. I don't know.
But it's divergent enough from what we'd naively suspect to justify exploring alternatives.
I think part of what is frustrating to me about your phrasing here is I don't understand why you are using "naively" as a good thing. Because, I'm not saying that this is the Rock Anima held by some rock-monster. What I am saying is that your expectation of wood and lush jungle life is a strange bias. After all, if Coyote's Throne was to be found in Death Valley in the heart of a desert, would you expect it to be a lush jungle paradise? I wouldn't. Coyote's don't live in Jungles, and deserts aren't where you find Jungles. It would be more unnatural to find that.
Yes, we should explore alternatives, but that also means not dismissing ideas as well. This Throne of stone, ice, and deep waters, with accents of living metal, rubies and sapphires may be completely natural. Not as some weird rock thing, but as an expression of a natural area of stone, ice and water with mineral resources.
"Beryl used her keen understanding of the Anima Thrones and her swarm of loyal mind-controlled Shamans to build a synthetic mockery of an Anima Throne and use it to wrongfully usurp the power and mantle of one of the real Anima Thrones" would not be surprising.
And as you yourself pointed out, Endymion went to all the Anima Thrones he knew about. Since Beryl didn't take the convenient opportunity to snap up her mysteriously resurrected grooming victim, it seems likely that Endymion didn't visit the place Beryl is camped out.
So if this throne is, as you speculate, a 'normal' Throne but of something other than the Anima thrones, it seems likely that Endymion didn't know about it, because for some reason he did not go looking for it on his world grand tour. Since Endymion seems fairly knowledgeable about pre-Fall Earth, that in turn suggests that some other, seemingly less likely origin story would have to explain this Throne's presence. It would have to have been hidden from Endymion but not from Beryl, or have to have arisen after the Fall, or something.
Sure, it wouldn't be surprising if she, theoretically, had made a false throne to usurp the power of a real Throne. But that isn't what is being described. Naru can tell by looking that Beryl isn't supposed to be on this Throne. If the Throne itself were false, then she would likely describe something parasitic on the Throne instead.
My biggest issue with this being a Throne Beryl constructed is the issue of why she doesn't fit the Throne. Naru does have the power of life, so maybe this is unfair, but she has specifically realized she could create a lifeform that would fit the Throne. She has also realized that she has met someone or something that would fit the Throne. Beryl was able to build a Throne, twist life in the form of the Youma, but has been incapable of fitting herself or something else into the Throne? That doesn't sound right to me. The descriptive language is not giving the feel of an unnatural Throne held by an unnatural being, or a parasitic Throne taking over for a natural throne. The language is very much pointing to a natural Throne usurped and occupied improperly.
Now, as for why Endymion didn't come to this Throne, as you said, there are some theories. The first is that this isn't an Anima throne, but something else. Considering how close it is to the sign of Sol, and we know that the Earth is protected by Sol somehow, I'm fully willing to accept that theory. It is also possible that since Beryl and the Shamans were the only people to normally visit the Thrones as part of their diplomatic missions, that they kept one secret. It is certainly not impossible that Marduk and Beryl worked together to keep a royal secret from Endymion "until he was ready".
After all, consider, we have zero evidence that Serenity knew about the Anima. These Thrones might have been secrets from most people.
We've had it theorized that the World Tree may be a thing that has many instances in many different places on Earth. That would make sense in a way; we know the Norse, for instance, believed that the World Tree connected multiple worlds.
Now, the Norse didn't know that much about geography beyond their immediate region. And the only thing that might reasonably be mistaken for a "World Tree that grants access to other realms" is in Japan, somewhere nowhere near the Norse. Which doesn't mean that, I dunno, Odin couldn't get tipsy and tell some skald about it. But it does suggest the plausible hypothesis that there are many instances of 'the World Tree,' all of them somehow connected, that the Norse knew one of them, and that Beryl's throne (be it an Anima Throne, a synthetic knockoff of such, or something else entirely) could somehow be connected to an instance- either the same one or a different one.
Endymion might have visited one or more instances of Yggdrasil, but not all of them- perhaps because he thought he could learn everything he needed to know at that one instance, and save himself a lot of trouble.
Possible. Though, we really don't need the Norse involved in this at all. Heck, guarantee that Odin knew more about the world than just northern Europe. I'd also posit that we do not know where Yggdrasil or the Rainbow Tree are. Our only clue is a floating island, nothing says that floating island is stationary near Japan.