It's not logical given what we know of Zenos's character and his purpose to fight us.
You don't even need to frame it as good vs evil if you don't want to. We still have two opposing sides.As for the third section true that it could be totally different, I'm just spitballing the twist because I personally do not find good vs evil very fascinating as I don't think it represents most situations (I mean there are of course people who've got a screw loose and just really don't and cannot care about others, but that's not the norm). They're palpable stories but it's just not super interesting, to myself (so I am purposefully trying to find means to mess that up). But lets go on that line, so say Hydaelyn was made to keep Zodiark in check- right, right. How do you keep order in check? Chaos (freedom). That she was made to counter Zodiark doesn't really disrupt my suggestion that they may represent greater concepts than Zodiark bad and Hydaelyn is simply anti-zodiark. Then on Zenos, well I think Zenos is literally one of those screw loose people lol- so it really doesn't matter to Zenos about balance, the dude has been pretty frank to us in what he enjoys about life and right now he wants to make us dance with him. IF anything he might find it more enjoyable that he takes our mother and we have to join with Zodiark (father) in order to compete. It also might offer decent imagery as we in effect have to choose between saving everything or not beating up 'mother'. Like if some poltergeist took the body of a loved one and began to cause massive issues, do you stop it or do you bend knee?
My point is that the WoL is connected with Hydaelyn. So if Zenos goes after one of them (Hydaelyn or Zodiark), and again, we don't even know if that's where they're going with the story, then it would make more sense for him to go after Zodiark.
Zenos may be unhinged, but he still is consistent with his purpose.