Here we go.

1. Dynamis and Aether are just different forms of matter, analogous to real-world dark matter and... regular matter. The universe is composed of both (though it's actually, iirc, 2/3 Dynamis), though Aether overpowers Dynamis unless the latter is extremely concentrated. Primals are basically just aether engines; crystals are just highly concentrated forms of aether, which is why primals like them so much. The inhabitants of Ultima Thule are Dynamis-based recreations, but have some amount of Aether once the story gets rolling.

2. Yes, although there's a couple of wrinkles: they aren't primals like the typical kind we fight, instead being closer to "true" creation magic lacking the drawbacks of the primals summoned via the Ascians' rites taught to people in contemporary times; and they use the souls of Venat's collaborators as a base.

3. Not clear. Wherever they were beforehand; unless it's a named NPC you can think whatever you want.

4. I'm going to need a little more clarification, because I don't remember the Omicrons resurrecting anyone.

5. Hythlodaeus and Emet-Selch are able to do what they do in Ultima Thule because... they're Ancients. Having not fully dissolved into the Lifestream yet on account of their (relatively) recent deaths, we yanked their souls out for one last favor. At that point they remember things as they were because death undoes the memory locks set in place by Kairos.