This is very similar to the way I've always pictured the Zodiark Vs. Hydaelyn fight, even before Endwalker; Zodiark's purpose is very broad and indistinct (it's hard to tell how much of the job they lumped onto the thing through sacrifices was part of its purpose creation, but even without that it's got a lot on its plate), and crucially does not involve fighting. Meanwhile, Hydaelyn was purpose-designed for beating the everloving crap out of Zodiark as a major part of her reason for being. Yeah, she had other tasks too, but winning a fight was a primary objective, and since Endwalker confirmed she had the capacity to outsource at least part of her greater plan, she could put even more attention behind it.
It actually even carries over into their fights themselves: even granted that the Zodiark fight was being puppeted by Amon (probably fairly poorly), it's rather noticeable that Zodiark actually looks like he's bad at fighting. His only real means of direct attack are punches and some lasers, everything else is Amon using his power indirectly by creation magic and arena manipulation. He's got a lot of power, yeah, but very little capacity to use it in combat, and what ability he's got is clearly very slow. Compare to Hydaelyn, who's actually got combat techniques and some level of agility? She'd run rings around him, he wouldn't have a chance. ...which makes complete sense, actually; of course the primal made to fight Zodiark is gonna have advantages over Zodiark.
And while unrelated, writing this post just made me realize that I'm not sure how to approach Zodiark pronoun-wise. Hydaelyn was always a female form controlled by a woman, so that's easy, but for a long time Zodiark is basically just an empty mech suit; I kept wanting to use 'it'. The Ascians went for male pronouns, and I guess they're the authority, but there's point where that feels weird.