It's the first Primal we see in Heavensward when we rescue Emmanellain from the Vundu or Gundu or whatever the bad fat yagudo are called. So it was around probably before we even set foot inside of Ishgard, at a minimum.
When I first met Haurchefant and he was warm and amicable to the WoL I knew he had scriptwriter's doom. It took a couple years, but I did slam my fist on my desk when it happened.
The real reason Haurchefant died though, was because the side cast for the WoL in Heavensward had to be discarded by the end of 3.0 to make room for the return of the Scions. This is why Ysayle had to sacrifice herself to the dreadnaught. This is why Estinien is possessed by Nidhogg.
Stormblood handled the side cast similarly. Albeit a little differently since there were more of them, but more or less... Lyse leaves the Scions at the end. Yugiri returns to Lord Hien's service full time. Gosetsu goes down with Doma Castle and is presumed dead.
Shadowbringers is the first time nothing happens to disbar the side cast, because it's the Scions, though I suppose you could count Emet-selch if you wanted.
(Also when I say side cast I guess I mean traveling companions.)
The theoretical alternate timeline doesn't really go into the specifics of anything that happens after Haurchefant is spared like why Nidhogg is present to lay siege to Ishgard despite Thordan still possessing one of his eyes or how Hraesvelgr ends up bound by an Allagan neurolink.
You are actually presented with the choice of choosing whether or notto finish Thordan off at the end of the fifth phase, and the current assumption is that he needs to be spared so that he can help stop Nidhogg and Hraesvelgr at some point in their phase, but ultimately lay claim to their eyes and become the final threat of the fight.
Of course, the important thing to remember here is that in the reality of the game itself, DSR isn't an actual alternate timeline, it's the Wandering Minstrel weaving an elaborate 'what if'.
So when trying to make sense of the actual sequence of events, you need to ask the question of 'does the Wandering Minstrel actually care that much about worldbuilding?' Does he have an elaborate timeline of events planned out, or does he just think these fights would be cool?
honestly it makes me pretty excited for the future
like DSR is insane with its what ifs and the fight is almost a choose your own adventure book
what ever we get for stormblood gonna be insane
What if? Papalymo fails to seal Shinryu, who goes on a rampage in Ala Mihgo against the garleans.
Either we fight Shinryu at that moment or we hurry to activate Omega, who becomes part of the encounter.
Both ways would lead to Zenos coming out personally to fight against these potential rivals, and maybe even capturing them to prepare for the final encounter in which its Zenos+Shinryu+Omega or something like this.
My tinfoil hat theory is that to make up for the lack of the Warring Triad in an Ultimate fight, the three get added into a SB Ultimate - but not Kefka. Instead it's another What-if scenario where Regula successfully ships the Warring Triad back to the Garleans and Zenos uses them in combination with Shinryu. Thus adding more mechanics and phases to Shinryu who doesn't really have much more to add on his own aside from a Zenos doorboss-style duel and what the EX already had, without having to dip into Omega or try to very awkwardly shoe in Susano or Lakshmi or Tsukiyomi.