So today by default yarn goes through its servers which then proxy to npm's. As time goes Facebook can add more features to its own repo (custom submissions instead of to npm or maybe it does a federated publish to both at first, nice looking pages with community engagement tools built in, better metrics (npm provides me with almost worthless metrics), etc). Then when enough people are using Yarn Facebook could simply...flip the switch. Then boom, zero npm usage.
I would be terrified if I were NPM right now. They've sat on their hands for years not improving npm. I mean npm3 had a silly CLI animation that made all downloads take orders of magnitude longer simply because of the animation!
P.S. if you're trying to use yarn with a custom npm repository just drop a .yarnrc file into your project's directory then add the following in that file:
registry "http://<my register>"