Fitting for Endwalkers, don't you think?
Really, though, it's just that you won't confront the truth. The shards don't count as saving the world, because they are merely 1/14th of the world, and if they are Rejoined, then they are still part of and restore the world. The only way they are possibly lost is through a Flood, as the Ascians did the the 13th(and even then they're hinted at being salvageable somehow from Unukalhai void quests, being a monster farm until then).
With having never been given the knowledge to know what they were actually contesting, Team Hydaelyn, in the form of Ardbert's team, precipitated the Flood of Light on the 1st by slaying an Ascian Prime with a Fivefold Blade of Light. Team Hydaelyn on our end put a stop to it by being given information from the Ascians, not Hydaelyn, then begging for Hydaelyn's intercession but merely receiving Hydaelyn Amp'd Minfilia. One wrong, one right, all to attempt to stop and realign for a Rejoining. A Rejoining that goes on in the first timeline to succeed.
After which, a team that could at best be said to be, "Team WoL" goes about creating a time machine whose power source was made by Ascians, its spatial teleportation by extraterrestrial machine, and its time travel component by a good natured primal. All unaffiliated with Hydaelyn, as well as not guided by her. So they allow us to save the 1st, but in so doing we killed Fandaniel's leash handlers, which has now placed all of the world into jeopardy, since his long term goal, as of now, is total destruction rather than restoration. It's almost like history repeating with us in Ardbert's shoes now that he's literally in ours. And I won't count what the game hasn't told or shown me, even if I did count saving shards from Rejoinings.
So moving onto my crown, shall we?
Despite all his bluster about 1,000 years of prayer, Thordan was a wimp. He not only absorbed Lahabrea, he did siphon some of the Warring Triad's power in the middle of the fight to fuel Ultimate End. It did jack shit to the WoL. In our hypothetical he wins there, and then drains the rest of the Triad's power... maybe. Remember he would also get the second eye of Nidhogg. Who wins that contest of wills? Do we suddenly get Thorhogg? Well, we'll just say he gets another empty eye, so he can hold all of the weakened Triad's juice.
Remember though, they are weakened from 5000+ years of captivity while being used as floating island chain fuel. The danger is that they get out and absorb each other. Each has a simulation about if that happened, so we actually have faced the Warring Triad as a whole in each of their Extreme encounters. Proving ourselves stronger than that, too. So in this thought experiment, Thordan is the one that's stronger than that. Well... guess what. Zenos was stronger than us by far, beating us twice, once after us having grown stronger. So he was more than strong enough to contend even with a fully amp'd Triad primal (thus my intense frustration my first time through Stormblood). Strong enough to contest fully amp'd Thordan. What's more, is because he learns all on his own that he can mantle even very powerful primals using the Resonance, once Thordan tries to temper him, because why would a Garlean be resistant anyway, Zenos resists weakening Thordan. So here we get ThorZen or something, because Zenos would mantle the crap out of him like he did Shinryu. But even if Zenos loses, that means a severely weakened Thordan who likely loses to the rest of the empire, probably to a dreadnaught or other similar big thing. So either way, no planetary destruction. (Alternatively, if we go the ThorHogg route, we possibly get another primal that wants to protect the world but kill all Ishgardians given Nidhogg's duty/life).
Galuf's notes on Eureka are theoretical, and the notes specifically say to keep Eureka sealed forever. The danger is someone discovering it, and then using it for a large act of creation once they realize its true power. Without our intervention leading Ejika to be enthralled, there isn't even a risk since the WoL's intervention is required for the next exploration teams to even succeed. It's another case of, the heroes trying to do good actually causes harm(although in this case it's, the heroes helping some greedy merchants causes harm). By restoring the aether network as we did, we allowed the Primal Eureka out. In our Echo vision after we destroy its avatar, we also learn that Galuf and Co. are responsible for finding Eureka in the first place. Which, until they unearthed it, was sealed and not a danger.
So, sure, I guess I'll concede that we saved the world from Eureka... but we're also responsible for letting it become the threat we have to stop. That's how self contained stories go. And it should be noted that the softer player choice is to merely reseal it, allowing it to continue to be a passive threat to the world. So depending on player choice... there's no saving to be had. I for one, chose Ejikka's path, so that I could rectify my own unwitting blunder.