I was able to get a male dragon to show up once, but I couldn't tell you what made it happen. It's likely it prefers traditional lady anatomy, but it does conform to preferences to some degree. In my efforts, getting a flat-chested dragon with a peen took setting my preferences to encounter only flat-chested monsters with peens, but not knowing what's going on under the hood makes it difficult to know if that's outright required.
Edit: Thanks to the first dragon I encountered since making this statement, I can confirm that the pigeonholing I resorted to before isn't necessary for the dragon's anatomy to vary.