The launcher can run at any phase and start to download/stream tools and run them. Even if the launcher isn't complete or at 10% or whatever it may be, files will start to get updated to Blizzards latest patches, tools, scripting system, etc..
In fact, (this part doesn't relate to you) but... Some players have had a perfectly running and healthy 434(15595) client running for a very long time, and became curious by running the Launcher (God knows why they did that), but at any rate, before it got to 5% it had already corrupted the client and the player is now doomed to start all over again.