The References/In-Reply-To headers match each other, but not what I thought Discourse was using:
Edit:
I looked through some of the mail I’ve gotten from Meta, and see that the message IDs match the description given above:
From: Jay Pfaffman <meta@discoursemail.com>
Reply-To: Discourse Meta <meta+785bdce[ ... ]@discoursemail.com>
To: [ my discourse email address ]
Message-ID: <topic/59203/270905@meta.discourse.org>
In-Reply-To: <topic/59203/270854@meta.discourse.org>
References: <topic/59203/270854@meta.discourse.org>
<topic/59203@meta.discourse.org>
So, yes, I think the threading issue might be related to the Message-ID
getting replaced.