I have confirmed this with a change to config/locales/server.en.yml
user_posted: subject_template: "Re: [%{site_name}] %{topic_title}" text_body_template: | %{message}
After that, all mail messages (including the first of a topic) have the “Re:”, but Mail.app does properly thread them. So if I can figure out how to detect which posting is the original one, then I could make a patch for this. I’m also not really certain when the other mail messages formats are used (user_posted_pm, user_mentioned, user_quoted, user_replied) and whether “Re:” is appropriate for any of them.