In more detail; SMTV mainly deals with themes involving The End of History (based on the
book) and The Fall of America/The West. SMTV asks the question that, assuming American dominance over the geopolitical landscape were to end, what would Japan be doing next (a theme not unfamiliar to megaten; SMT1 asks a similar question in the form of "what should Japan do after WW2", just that SMT1 had the benefit of hindsight, while SMTV is more speculative).
You can see this framed pretty clearly in terms of the demons associated with Bethel and the directions they take once Arioch falls and God is all but confirmed to have died since the Nahobino exist once more. Odin and Zeus both represent Europe and when it becomes clear that YHVH is actually dead, they both go back to their own areas in the world of Da'at. Europe would have a lot to lose from the fall of the US, but both are ultimately safe from it due to their power predating that of the US - they're unlikely to fall apart from it. Meanwhile, Shiva and Vasuki both represent India; a country with much to gain from the West falling as it's unique economic growth over the past decades has granted it a position of pseudo-world power, but diplomatically, it's not strongly affiliated with the West nor is it strongly affiliated with the Wests enemies and it's been able to grow into an economic powerhouse regardless of either. It's why Shiva doesn't even bother showing up to the Bethel meeting - if the world is going to end, he'll just do his dance to ensure that no matter what, the Indian gods will have their place in the new world; from this comparing perspective, India will likely be fine, no matter what.
The only one who doesn't fit neatly is Khonsu and this is where the games troubled development cycle becomes a problem. Khonsu is on paper affiliated with the Egyptian branch of Bethel, but already immediately abandons the throne because he sympathizes with Miyasu. A lazy read would be to assume that he's meant to represent Africa - a continent that even in the face of a Western collapse has very little to gain from it's collapse and also very little to lose since it likely won't be a world power regardless - the continent is still developing. The more interesting angle is combining his plotline with the games Neutral route, which is clearly intended as you need to clear Khonsu's sidequest (alongside beating Shiva) to unlock the True Neutral ending. Base SMTV's Neutral route is chiefly represented by the Chinese mother goddess Nuwa and the resident Raidou callback - Yakumo. It is not a surprise that Nuwa is picked here - if the US were to fall, China is easily the world hegemony slated to replace it. From this perspective, Khonsu's affiliation with Africa becomes much stronger;
since China has been accused of neo-colonialist behavior in Africa and Khonsu's abandonment of the throne and his sidequest being required for the True Neutral ending play into this idea. Khonsu is unfortunately just underdeveloped, so much of this remains speculation.
And that finally leaves the Christian branch, the Japan branch and Chaos (the enemy "faction" led by Arioch, although it's organization is poor). The Christian branch is easily explained - the remains of YHVHs army, now trying to keep a faction of myriad Gods they'd otherwise have hated and would have crushed together. Abdiel is the extremist position among them; she believes that she can just beat the demons using the strength of the angels alone. The game goes to... rather extreme lengths to prove how delusional Abdiel ultimately is however - the Bethel branch meeting cutscene might as well be an extended takedown of her beliefs. If we stick to my previous analogy, the Christian branch is the US, desperately trying to keep itself together after the fall of it's dominance. Abdiel in this perspective then represents the kind of ultranationalism that is pretty common in the US.
The Japan branch meanwhile is... more difficult to explain. It's quite clearly meant to represent Japan as a whole, however it has been all but decimated after the fall of YHVH (in the analogy - Japan has a lot to lose on the world stage if the US were to fall and it being considered a world player has hinged a lot on the US). Unlike the other branches, who are represented by major gods in the pantheons present in those regions, the Japan branch is represented by the core faction representatives, the protagonist, Tao and the pair of proto-fiends that are Aogami and Koshimizu (who the game elaborates on are Susano-o and Tsukiyomi. This doesn't fit in cleanly anywhere else but I just want to mention quickly that Aogami in particular has some superhero elements to him - Susano-o and Tsukiyomi are both Japanese gods who are often used in popular entertainment, giving them both the idea of a "fictional hero".) Tao is mainly neutral; she'll guide the player no matter what and both the faction representatives are underdeveloped in this game (likely due to a bad development cycle). That mainly leaves Koshimizu as the one carrying the main idea behind Japan branch's analogy/wishes: Koshimizu wants to declare that God is dead, under the belief that a world of myriad gods all working for themselves is what will allow Japan (and the rest of the world) to thrive. (This is almost stated verbatim in the game). This is why he ultimately represents the Chaos faction in the endgame the best and really Chaos as a whole; Arioch wanted the same thing as Koshimizu did, but couldn't organize the demons/scheme enough to bring it about (which is why the few organized Chaos demon generals are all representative of minor religions; a basic example would be Chernobog, a demon based on an eastern european god of misfortune). Koshimizu had to go in solo to pull it off.
And that brings the endings: for a brief summary of them: In Law, you take the throne and make a new world under the rule of the old world in the hope that YHVH will some day return, in Chaos you create the world of Myriad Gods, in regular Neutral you destroy the throne and leave nothing in it's wake and in True Neutral you destroy the throne but remain in it's seat to prevent any gods from appearing ever again as a new world is made regardless.
Law is essentially just hoping that some day, the US' world hegemony will return, although the game is pretty explicit that there is essentially no hope of this ever happening. Chaos meanwhile brings about the world of myriad gods, but it does so under the admittance that all bringing this world about did was create more strive (befitting for Chaos). Regular neutral is considered negatively by the game - the game all but calls you a chicken for not picking any option and notes that the lack of creation of a new world will just mean that the current world will fizzle out.
True Neutral meanwhile calls back to 4: Apocalypse and sees you remove the influence of Gods and Demons from humanity. It doesn't go the full nine yards and tell you that this is the best ending possible - the downside is that Gods and Demons have clearly influenced human ideals and beliefs and letting go of them means actively killing your own beliefs (something the game draws attention to with how it also requires getting rid of Aogami), but it's pretty clearly favored by the developers due to how difficult it is to get.
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