I've never seen a 650B tire appropriate for CX. That doesn't mean there isn't one, but 650B availability is less than any other size I know of, and I've never seen one with a tread pattern suitable for CX.

Disc Brakes are not legal for CX racing, last time I checked.

Martian Destiny:
Why do you assume 26" equals "mountain wheels?" What does that mean?
You can easily build a very nice, responsive, and well-fitting CX frame that will accommodate 650c (road) and 26" wheels--I do this all the time. It wouldn't have to resemble a "hardtail" in the slightest. 26" wheels don't need to be "mountain wheels." Go with a light velocity rim and 130mm road hub of your choice, double butted spokes...handbuilt and very sweet. My 26" CX wheels are the sweetest wheels I own, and lightest. There are also excellent, light, kevlar beaded 1 inch slicks (25c) that come in 26". If you are going custom you are welcome and usually invited/encouraged to think outside the box a bit.

Honestly, possibly the best advice I have: listen to whatever framebuilder you've chosen advises. If you trust the builder and they are experienced and know how to make a bike that really fits, s/he will take care of you.