Because manual flash doesn't play nice with E-TTL pre-flash metering etc. Which can trigger the main flash on the pre-flash even if the guns are set up manually.
If you're using optical triggers, sure, but why when RT is so cheap.
I have the same setup as the OP, plus a YN 460 and YN 565 (I think that's the model number), and I've never had a problem with any of my Yongnuos with my 6D or the camera before that. Not saying that Yongnuo hasn't had some quality issues, and Canon flashes are undoubtedly more reliable, but not to the level you make them out to be. Third party products have their place, I'm glad for the open market that allows them.