There is a crystal formation beneath the platform in the Dark Inside that appears to be this "father crystal". It is, presumably, an equivalent to the mother crystal formed out of Zodiark's aether.
The entirety of the events leading up to the Word of the Mother thing always felt contrived and they've never really explained well what happens there.\
Zenos is just that strong, as is Ran'jit. You have to keep in mind, the Warrior of Light is not all powerful. They are strong, martially and mystically, but not unmatched. They often have to have friends along them to be able to defeat their biggest threats, or be empowered in some way. Zenos was explicitly stronger than the Warrior, literally 10 levels stronger than them in gameplay terms. Note how Concentrativity initially acts as a fight ender but eventually "becomes" a raidwide AoE. Similarly, the Warrior never actually loses to Ran'jit, the fights either get interrupted or the Warrior gets stunned. Ran'jit has been fighting against sin eaters for nearly their entire existence, and was trained by his father in now lost eastern martial arts. Beware of an old man in a profession where men usually die young and all that.
This is, to my view, most likely a mistake. We have like two extra Ascians in that bit, since Emet Selch is meant to be taking a nap too. Exposing an Ascian to the lifestream in that way seems like a surefire way to kill them.
This quote, I think, was him talking about why he even came out of Zodiark. There was a great divide among the ancients after the summoning of Zodiark, and Elidibus, as the envoy, was needed to reconcile both sides. This was Elidibus' (the title) role in the Convocation, and he tried to stop the conflict.
We see how Mikoto's future sight was limited and uncertain. She was sure that she would die in that airship but was saved because she didn't have the whole picture. Being able to see the future means nothing if you can't see all of the future.
They might come back to this eventually, but yeah, presumably they're out there.
This one is definitely a case of them setting up something then plans changing. Still never really explained.
Ultima, the High Seraph, is an interdimensional being that creates auracite. Presumably it also created the Heart of Sabik, as implied by the questline. Ultima is explicitly said to not have a sense of self until it was worshiped by mortals, eventually gaining sentience in a manner like a primal. Basically, a primal summoned on an existing being, not dissimilar to Shiva summoned on Ysale or Alexander summoned on the remains of buildings. It's just that Ultima, the High Seraph was summoned on the interdimensional being known as Ultima. They might still expound on that but it's not that unclear, I think