Actually Origin has been doing this since the beginning. I have 2 Bad Company 2 copies, one I bought in a shop and the other was on Steam with all the extra stuff. I have never activated the one on Steam, instead I used my old one's key along with the keys from the extra content. But since the beginning Origin knew I had 2 BC2 copies.
I was curious what would happen if I install a pirate EA game, so I installed Sims 3(the only pirate game I could find and the only one I wouldn't normally play), but nothing happened. I left it there for 2 weeks before I formatted my PC.
So while Origin magically know what game you purchase in digital format from another vendor, it doesn't react to a pirate game.
But let me know when a game I buy in a store magically appear on Origin...