Zenos still needs a god to latch onto. Unless he's planning for it to be Hydaelyn (doubtful, but either way he'd need both), he now has a vested interest in the Rejoining and revival of Zodiark. He would not use the Black Rose if it killed you off, but that does not mean he would not utilise either it or the Empire in pursuit of his "hunt" - if Elidibus is successful in keeping you mired on the First (that could even involve finding a way to get Zenos there) whilst Zenos also uses the Empire to prepare the Source for a Calamity required to resuscitate Zodiark, I could easily see his professed aversions melting away.
I personally don't think there's any obstacles to Zenos's claim, other than Gaius bearing witness to it. His death meant Varis had no reason to disinherit him, and Elidibus's use of his body would also run counter to it.
Which isn't to say I think he's a good character, but he could certainly play a very big role in the story, depending on how Elidibus himself moved the pieces on the chessboard.
If true, it's all too convenient, to me.
I also don't necessarily buy that that's what he's getting at, if Cilia's reference point is his Praetorium dialogue. He refers to a growing imbalance. Yet the Sundering was, as far as we know, a one and done event upon Zodiark's defeat. That moment did in fact render all existence unrecognizable to the Ascians, fragmented and broken. His contention is that her continued presence in the star is what will warp said laws. Unless she is continuing to sunder and dilute the world (which creates its own unique array of problems, if true), his contention remains a mystery. She has already fragmented all existence, barring the unbroken members of the Convocation, and the protagonist as they progressively regain their "fragments" - for all intents and purposes, "Creation magic" as we know it is gone. For what you suggest to be possible, she would have to completely shatter all consciousness, because what yields Primals is belief/motive (usually collective) and adequate aether to be shaped by that belief. Or alternatively (and taking the other fork in that pathway), diluting aether until it becomes worthless for such purposes, but scarcely unproblematic since virtually all existence is constituted from it. After all, if even beast tribes with no distinguishing talents/traits can summon Primals, given adequate aether, that is enough to deduce (based on our current lore understanding) that it's not driven by the possession of Creation magicks. It's just that the Ancients possessed such deep wells of aether that they could themselves, at an individual level, manifest such beings, without the need for extrinsic aether, and this appears to be what they termed "Creation magic". Whereas he is referring to the twisting of laws both aetheric and physical, which sounds closer to something affecting the star itself, if he is right.
Whilst it's possible that the underground monstrosities were the result of another group of Ancients, with Zodiark then probably being summoned to restore the world and reassert control (perhaps through the act of tempering), there's enough in the setting to allow for the possibility of completely alien/otherworldly parasites, too, and it would not be the first instance of such warfare/invasions we're aware of in the setting, as well as parasites that have always lain dormant in the star.
I'll agree that there's a lot of unknown variables, but I don't think that the elimination of creation magic is all that he's getting at - unless the enervation has not ceased. That would be interesting, but again, it's a big "if" for now.