I think players should take better notice of the FFXIV story as 6.1 revealed the FFXIV version of Atomos is actually a type of non-sentinent voidsent, specifically it's an odd kind which possess a Voidgate within it's body that allows other voidsent to enter the Source (Y'shtola creates an artificial one in 6.2's main scenario, that the Scions use to brute force the hidden voidgate in Alzaldaal's Legacy open to allow multiple people to enter it at once). Several show up in the Crystal Tower raids earlier in the game as well (again fitting because that also involves the void).

FFXI's Atomos is something completely different, so that would be the clue that this new raid is even less likely to feature the 'real' Vana'diel... and simply be more Hydaelyn-based areas referencing Vana'diel areas in names and themes.