It's more just how Xibalba functions and how ludicrously unbalanced it is at times, and how thematically they're basically just Mictlan again. I recognize most of the different mythical influences, and I think it's a pretty awesome thing to pull ideas from.
I mean... Of course I see how Vanheim and Jotunheim are both centered in Norse myth, but they represent two distinct sides in Norse myth, namely the Ęsir/Vanir vs. the giants. The details are of course quite a bit more complex, but those two sides are specifically and distinctly represented in the original myths.
Xibalba, meanwhile, is... Mictlan. It's the mesoamerican underworld, which Mictlan: The Nation already represents with its demonic influences/summons.
I'm less up-to-date on celtic myth, but I believe Fomoria/TNN are another perfectly reasonable pair founded in the same root myth, as they both represent different "sides" and thus embody different aspects of the whole.
It's more the pairs like Vanheim/Helheim that I don't understand, because I don't see how the end nation is really distinct enough from the other to be interesting and I at least can't recall any particularly distinct factions or powers in nordic mythology that Helheim would serve to represent... Hel was a half-giant daughter of Loki and she pretty much had full say over whatever went on in her domain, so reasonably she'd be associated with Jotunheim (as newly represented by the Draugar summoning spell available to them).
Pangaea/Arcoscephale is another pair I can "get", seeing as they're representing the civilized versus the uncivilized aspects of Greek mythology. Actually, it's more of a kind of split between Greek myth and Greek history, but still...
Berytos are pretty clearly Phoenecians, and while they're the only ones specifically based on that, there are a lot of overlaps between (what we know of) those beliefs and the other mediterranean legends, and as an in-game nation I really just don't see how they're supposed to stand out. They're really just Gath with some palette swaps.