I actually know a lot about FSA's story. I've had it relayed to me, plus I've read up on it on Wikipedia. I keep telling myself to buy it, but it'll cut into my college funds. I'm not saying Aonuma is correct or anything. For all I know he just made something up on the spot. But it's the only definitive thing we have into the creator's minds. If I had to harbor a guess, I'd say that it seems like it's in the middle of the timeline because they reused so many familiar Zelda staples. In fact, they admitted not only that the game uses a LTTP art style because so many members from the LTTP team worked on this one, but they intentionally reused familiar things from past Zelda games so fans would recognize them. So perhaps nothing in the game has timeline significance. Perhaps they'll just let FSA hang out near the beginning and never touch it again. That would be my guess anyway. And FSA isn't supposed to be an origin story. It's supposed to be the culmination of the Four Swords saga.