Sorry for digging this post out of the grave but I have a quick question. It seems that most custom domains get hit with Medium's blanket nofollow for non-medium.com domains. This ends up destroying SEO as your site architecture gets screwed.

I noticed that the three publications with custom domains that you listed in your post all are dofollow though. What I can guess is that Medium is whitelisting some URLs to be dofollow? It's weird behavior...