I personally would not use a different ball size for rebuilding that hub. Bearings are cheap enough, and you should be able to find them at another shop, or even online for just a couple dollars. Heck, go all out and buy expensive "premium" bearings for a smoother hub...the difference is negligable at best, the bearing race having as much to do with quality as the bearing. The RX100 was a cheap hub and you should only expect the according quality.
As for the cones, it looks like a manufacturing defect to me. There are several compatible cones available to fit the RX100 hub. Nice compatability
chart here.