I think the Twelve are more closer to the classical Zodiac than the actual Greek pantheon, but even then it's a very lose association. I guess like a lot of the basic worldbuilding for 1.0 it was done in a very vague way that is still wrecking havoc years later in ARR as the current writing and lore teams struggle to expand the story without contradicting existing information (watching the lore panel video from the first Fanfest Ferne admitted that the original worldbuilding/lore creation for 1.0 was handled by a staff member who longer works for SE and thus they're basically having to go through and fill in the blanks so to speak).

Like the Garlean Empire being based more on ancient Persia than Ancient Rome, the Twelve being roughly analogous to Greek gods and goddesses might be on of those things that inadvertently changed in the long period between 1.0 and ARR's development.