After sanding off the spots, it looks like he stitches the joint as-is (as opposed to reinforcing with fiberglass first). Is the CA glue that strong? Also, which CA glue should I get - there's thin, medium and thick. I'm assuming I should get the medium..

The CA glue is strong enough to hold the boat together until the glass is applied. It is not super strong, but strong enough. Don't think about strapping the boat to the roof of the car and driving cross country, but you can carefully pick it up and move it.

I use a somewhat thick CA glue http://www.caglue.com/Special-T_c_17.html which is thin enough to wick into the joint, but thick enough to bridge some gaps.