Setting aside that Zenos's actions were oft based on his father's (lack of) consent—why Zenos didn't attack the Wall, resorted to baiting the Alliance deeper into his own territory, went to Doma even though he didn't want to (and bailed as soon as Shinryu was found, saying that he'd fulfilled the letter of his orders and was thus beyond Varis's reporach), and was allotted a massive R&D budget on tech that is coincidentally exactly what Elidibus was proffering—I would argue that Elidibus's lines at the end don't leave an abundance of wiggle room for what the Emperor was ignorant of.
In other languages this line is rendered as "Are you so ruthless a man that to raise an empire that would dominate the entire world you would even sacrifice your trueborn son on the laboratory table without difficulty?" That Varis didn't have any questions about that (otherwise vague and ominous) phrasing leads me to infer that was well-apprised of the XIIth's actions.Elidibus
You do not mourn his loss? ...You surprise me, Your Radiance. He was your son and heir...and an irreplaceable test subject.
Elidibus is amused by Varis's conviction and assures him (when Varis threatens to hunt the Ascians for teaching the tribes how to summon primals in the first place) they are both acting in service of the world's salvation. Elidibus assures Varis that the only way to save the world is to "change it" via the Rejoining. Varis leaves it unclear whether Elidibus implied or explicitly said that the only reason he intends to awaken Zodiark is to force His reunion with Hydaelyn, but this is his impression and Elidibus encourages it.
Could it be true? Perhaps. I would argue that Elidibus sympathizers should embrace this as a core part of their philosophy. Perhaps, even directly linked to Zodiark's will, Elidibus doesn't have the same "burn Her out like a parasite" drive He instilled in the overlords. (It was directly stated that Zodiark gave Elidibus a unique mission) Extending from that, perhaps Zodiark truly wants to go home. Or perhaps Zodiark was unable to strip Elidibus of all of his mortality and he works within the exact letter of Zodiark's will while still undermining His end goals (as Elidibus has shown he's capable of doing to every other faction). Perhaps Elidibus is running a Gospel of Judas-level sacrifice and long-con as Hydaelyn's greatest champion. (I still hope he's a snake and goes full Time Compression and ends up the ultimate baddy, but hopes don't count.)
Notice this exchange, though:
Sound familiar? Flashback: Patch 2.1Varis zos Galvus
Compression. Resurrection. All is in service to your “one true god.” And when the sundered shards are made whole, will there be a place for us mere mortals?
Elidibus
Doubt my claims and question my motives if you will, Your Radiance. You will come to trust me in time.
Why would he echo the very same line he used when he admitted that whatever happens to us, we won't ever be the same?Elidibus
Your Mother favors you still, that much is plain. But surely you must feel it? Her influence wanes, and Her strength shall soon be spent. These lands, these people, this world─all shall soon change. As it was, so shall it be again. As it should always have been. Doubt my claims and question my motives if you will. Only believe me when I say this... I am Elidibus, emissary─bearer of the word of the one true god. And we shall meet again.
Should we feel comfort in assuming that these boundaries guarantee that either Zodiark wants to be reunited with Hydaelyn or Elidibus is a liar? Or what if Elidibus is only correct in saying this by technicality. Zodiark is stronger than Hydaelyn - what if being reunited with Her simply smothers her out? "Burns her out like a parasite" if you will. Or what if Elidibus was only ever referring to Zodiark being reunited with the planet Hydaelyn, leaving the Mothercrystal's fate entirely unspoken.Encyclopædia Eorzea
Nevertheless, his loyalty to Zodiark—the will within the Darkness—is absolute.