"A lot of that was in my head until we were starting Inquisition and the writers got a little bit impatient with my memory or lack thereof, so they pinned me down and dragged the uber-plot out of me. I'd talked about it, I'd hinted at it, but never really spelled out how it all connected, so they dragged it out of me, we put it into a master lore doc, the secret lore, which we had to hide from most of the team."
So, no they didn't know the "deepest secrets" of the lore 20 years ago. One guy had vague notions in his head, and they only actually fleshed it out when they were working on Inquisition.