I'm interested in this lore too, because the motivations behind Hydaelyn's summoning are a bit unclear to me.
Zodiark's alignment with darkness was a way to restore the flow of aether to the star after the final days began, due to dark's tendency towards change, but it seems that Hydaelyn's alignment with light was purely in relation to Zodiark. That may be purely as a way to give her the greatest possible power against him, but it also feels implied that the reason to summon a light-aspected primal would be to balance Zodiark's dark-aspected aether. Is there any evidence in-game that the darkness generated by Zodiark was a threat without a light-aspected primal to balance it? Or was it that Zodiark would require continuous sacrifices and aether, and the only way to prevent the steady death of the Ancients, and eventually the entire star, was to use a second primal to contain him?
Zodiark was sundered and contained on the moon, but his effect on dark aether was strong enough that it was the only thing keeping the star's aether flowing strongly enough to prevent the final days, and it was implied that the reason the moon is barren is that he's continuously draining its aether. Hydaelyn was always weaker than Zodiark, but you would have to assume she was also draining the star's aether. I've been under the impression that she gets it from the core of the star and its reflections; is it ever addressed whether that would cause harm in and of itself? Perhaps the star simply didn't show the effects of this because it's much larger and more aetherically dense than the moon?
Of course the fact that the lore of them being primals and the conditions of their summonings wasn't developed until later is relevant here, because it does feel like he was initially intended to be a manifestation of evil while she was the manifestation of good. With the events on the First and the Thirteenth shedding light on the actual effects of light and dark aether, though, the fact that an excess of either type is a negative thing makes their aetherical alignments more a result of circumstance than either being "good" or "evil". It ends up coming down to Zodiac's darkness being a result of his purpose (to encourage the flow of aether) and Hydaelyn's light being a result of her direct opposition to Zodiark. It then evolves into Hydaelyn's motivation being to prevent the rejoining and Zodiark's motivation being to facilitate it, thus aligning light with the Scions' cause and darkness with their enemies.
Sorry if this is a bit rambling, I'm kind of putting my thoughts together as I write them. I think the actual answer for why that ambiguity exists is just the fact that the lore is being developed over the course of the game's plot rather than having been developed beforehand, but it's interesting to think about how to work within the established information to make it more coherent.