Problem 47,383 of creating a game with this sort of branching story is that it becomes difficult to do any foreshadowing. After two levels of branching, the player could conceivably be on any of 6 social hubs, meaning that only 1/6th of the time would the player experience a particular foreshadowed event.
One of the ways we work around this is by making foreshadowing details serve alternate purposes as well. Early game conversations about luddites and Spartan civil war certainly allude to events that could happen later. And if you happen to hit on one of those specific events, awesome. But if not, then the conversations still serve a purpose in helping introduce some of the main NPCs and framing the first story-branching choice.
To this end, we've recently been working on act 2 rumors aimed at setting up 6-different transitions into act 3 (more on the act structure here). On the surface, these rumors will just be world flavor dialogue being provided by gossiping NPCs, but they'll each be setting up a specific act 2 -> act 3 transition.
There's still a lot to be done system-wise, from making sure rumors don't repeat (easy) to making sure you always hear the appropriate foreshadowing rumor on your way to act 3 (hard), but I'm confident we'll figure those out. Maybe we'll even have a blog post somewhere down the line explaining how.