"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.
They're trying to portray it as something that was done from the very beginning, as opposed to something they only pinned down in preparation for the 3rd game in the series. Nothing wrong with them getting through two games before writing out their bible, but that doesn't make for a very compelling article.