Emails are not threaded in Outlook 2013

No. You may talk about these headers:

In-Reply-To: <topic/16501@meta.discourse.org>
References: <topic/16501@meta.discourse.org>

It has been explained here why it is wrong:

In-Reply-To and References must point to a unique message id. <topic/16501@meta.discourse.org> is not a unique message id thus mail clients cannot do threading. It works when I replace these headers with its correct message ids manually on the imap server.

edit:
I had a look on a github email. They do it this way:

Message-ID: <discourse/onebox/pull/257/r20941543@github.com>
In-Reply-To: <discourse/onebox/pull/257@github.com>
References: <discourse/onebox/pull/257@github.com>

Maybe fixing the Message-ID in discourse mails suffices. Dicourse does it this way (wrong!):

Message-ID: <5475a885c34fd_2fd5036a24480ae@archvm.mail>
In-Reply-To: <topic/753@discourse.sevenbyte.org>
References: <topic/753@discourse.sevenbyte.org>