Souls are a plot oddity that needs further looking into - I'll be paying close attention on my second playthrough.
The short story "Through His Eyes" says that souls cannot be created but "spontaneously manifested within creatures that were born in accordance with the laws of nature [...] a gift from the star itself, long held to be impossible to recreate". Admittedly "long held" suggests that belief may have changed, but everything else points to it still being a fact and the phoinix's imbued soul being an accident.
Meanwhile in Elpis it's all about created beings and the small number of people experimenting with naturally breeding their plants and animals are shunted off to a side island we don't even visit in the course of the story.
Possibly the created beings are soulless but their offspring acquire souls, but I can't remember how it was talked about in the MSQ.
Though come to think of it, Alpha (and possibly Omega) seem to subvert the "only natural creatures can acquire souls" thing anyway. I'd say the ancients must be mistaken, but if they can see souls in the first place then it shouldn't be a mistake they can make.
I have to say that I am surprised we willingly gave them the entire story when only mildly pressed for it.
At least with my mindset of "must not break anything", I would have thought it sufficient to explain that yes, I was from the future as Venat had deduced, and I was here because the world of my time was facing a disaster that we understood had happened before in the past, and were hoping to pick up some clues about how the people of that time had dealt with it.
Rosenstrauch did a good job of explaining the larger picture of it, but the simple answer to this is - yes, Venat/Hydaelyn in the Eighth Calamity timeline would see her champion die without ever completing the time loop and fulfilling the purpose she hoped they would.
Her confusion is inevitable, but if our telling "the whole story" in Elpis included talking about the events of Shadowbringers and averting a foretold calamity, she may be able to deduce that she has ended up on the wrong side of the split timeline and therefore there is nothing strange about events not lining up. This really just means she needs to make a new plan and doesn't need to wait for circumstances to match what she previously anticipated.
What happens after that is entirely speculatory and not really relevant to making sense of the plot in this timeline.
I don't think the story needs to "establish" that the two timelines are on the same branch. That seems like the basic assumption to me, while the idea of them splitting into fully parallel worlds seems odd and much harder to reconcile with the known story.
G'raha travels back in time along a single timeline (as he knows it) and his actions cause a second timeline to branch off from the first one. It seems far more natural to picture that as a branching structure than a duplication of everything.
It's a good explanation. And yes, it's incredibly hard to put the concepts in words from the very beginning and not have people misinterpreting through their own different starting point of understanding.