One of the things that's fascinating about the twist at the end is the implication that basically all native lifeforms as we know them were created by the original power of the Amaurotians at least in part as an effort to repopulate the world after their calamities. It supports that any sufficiently-advanced civilization will (initially?) seem indistinguishable from gods -- and, their ability to create a construct that rewrites the planetary laws of nature (Zodiark) is itself a sort of proof.
Although we definitely got the sense of this all along, it puts into perspective why the Ascians generally thought of all planetary life as basically insignificant ants to be toyed with. Thanks to Hydaelyn, the natural evolution of their creations was stunted by having their aether fractured. The fact that so many of their brethren sacrificed themselves for this "imperfect" result is definitely a big part of why they kept fighting so hard for the rejoining.
Aside that, it's important from a narrative point of view that this come after Heavensward, as the dragon conflict sets the stage for the perspective of the Ascians. Nidhogg's thousand year war of revenge was because time flows differently when you're all-but-immortal -- a thousand years is like a day. Now you see it from the point of view of the Ascians who have been at this for "thousands of thousands of years" and you can see why they think of all life as we know it as totally insignificant. As they allude to many times, the scale of their perspective is completely different -- how can you get attached to anything so transient after seeing eons of generations come and go, especially knowing that this "transience" is a byproduct of a forcibly-introduced imperfection that could be destroyed?
It also leads to the point that both Zodiark and Hydaelyn were solutions based on the limitations of Amaurotian knowledge because of the one domain they hadn't mastered: control of time. Why would an immortal being care to study time? With time travel, Emet-Selch alluded to a much more elegant solution to his problem: go back in time to eliminate the "hero" Amaurotian entirely -- who, as others have suggested, is probably the 14th member and the one responsible for summoning Hydaelyn to start with. Of course, had he not been tempered by Zodiark, there was an even better potential solution to his problem: going back in time to stop the original calamity from happening in the first place. But given that the Amaurotians, in all their "infinite wisdom," still don't seem to know what actually caused it in the first place, they probably wouldn't know when to go back to anyway. (I like the theory that it was their own hubris and over-manipulation of aether that caused things to fall apart until they were able to give the world a new form through Zodiark.)
As for what to do with Zodiark and Hydaelyn now, the real question is just what is the minimum required to preserve the status quo of the shards and prevent massive loss of life. Because Hydaelyn was summoned to counteract Zodiark, there's basically no way to remove the former unless you remove the latter, and perhaps the reverse is true as well. But if doing so would threaten the stability of the shards, then it may be that they need to preserve both somehow. Can they usher the two gods into eternal slumber instead?
Incidentally, one of the most fun points is that the Shadowbringers plot provides seemingly-significant evidence to suggest that the Dotharl belief in reincarnation -- that the spirits of the fallen re-inhabit the lives of the newly-born -- may actually literally be how things work. (And actually a lot of Xaela beliefs, though distorted by time and tradition, are not so very far off from the apparent truth.) The previously-immortal souls of the Amaurotians (and the other life created by them) were sundered along with the world itself, and they continually reincarnate into new life as part of the reincarnation cycle. We already basically knew in a broad sense that this is how the lifestream worked, but the idea that souls would remain distinct enough to be linked even through the millennia really supports that the Dotharl are onto something.