I believe that Mail.app will only group the replies if they start with “Re:”. I would love to see an option to support this, as it is probably the single thing that is making me very hesitant to throw my lot in with Discourse and abandon YahooGroups - I (and others) need to be able to read and handle the support via email, and the lack of Mail.app grouping topics is a real killer (even if Mail clearly should be using other headers, but getting any changes from Apple is essentially impossible).
If someone can suggest a hack solution for this that I could try to verify that “Re:” would fix it, I’d be happy to try and at least ensure that is indeed the issue.