Corypheus also is completely confused on where he is or the time. Add in the Grey Warden accounts of him being there for roughly 2000 years, while the history of the Chantry (at least I think that's the correct codex) talks about Tevinter being destroyed from within after the first blight by rebels like Andraste. And that was 1000 year previous.
So, and I openly admit I'm using some personal assumptions here and freely admit I may be wrong, and there may be lore I have forgotten about, but here I go anyway:
The first blight lasted 400 years because no one knew how to fight the darkspawn and the archdemon without it possessing nearby darkspawn and re spawning itself. The blight absolutely ravaged the surface until the Grey Wardens arose. The wardens were able to drive back the darkspawn and defeat the blight. I'd give Tevinter maybe 100 years after that to restore its military and its crops, as it takes decades for the land to recover from a blight, and this was a long blight.
So that takes us back roughly 1500 years from current events in Thedas. But based on the Grey Wardens testimony on imprisoning Corypheus again, it was 2000 years earlier. There is a very big gap in the timeline; 500 years.
Did the magisters sneak into the deep roads? Possibly. Could they have created darkspawn? I don't see that happening as Corypheus had absolutely no idea what was going on or where he was. He may have forgotten a lot in his sleep, but he knew about his invasion of the Black City, which was already black when he showed up. He talked of how he was guided by Dumat, and wasn't intent on stealing the maker's power at all. He didn't believe in the Maker.
So were the dwarves the first darkspawn with genlocks? Maybe. We have a 500 year gap to allow the darkspawn to build armies. But if the magisters were the ones who created the darkspawn, then Corypheus should've been much less confused.
And where did the Grey Wardens learn their joining ritual or figure out how to fight the archdemon if the order was only created during the blight, but they existed to lock up Corypheus 500 years earlier than that?
My personal feelings are that the darkspawn taint existed or was created beneath the surface. It was the magisters and their ability to influence those with the taint that brought about how serious the problem could be, and a blight that shows how dangerous it truly is.
At least, that's my personal interpretation based on my memory of the lore and events from the game. As I'm currently replaying through the games, I'll eventually get there and I may end up proving myself wrong, but hey, you can't learn without being wrong first.