But wasn't the conflict that kept the Cloud of Darkness away based on Light clashing with Dark, as Altana herself said? Then what's the reason for Odin and Alexander to cooperate against something else (in this case, an adventurer that got CoD to manifest physically to punch her in the face)?
Before the CoD fight Alexander even says a moment like that (presumably their coorperation) would not happen again in the player's lifetime - maybe the story designers and combat designers weren't quite on the same page?
I guess they could always claims that the Vana'diel elemental forces might actually work better together - IIRC, fire, thunder and wind are light-aligned, while water, earth and ice are dark-aligned, so light+dark together work as concentrated "vana'dielness" to keep the winds of time running by having them clash against peak ability adventurers (who have beaten or equaled most challenges in the world so far) who were able to keep CoD at bay. That way the analogy to keeping the game alive as long as players have something to fight still holds...