When Jira processes a new received email, it can only post a comment to an existing issue if the subject line matches (both issue key and summary). But when Jira gets a new subject line that does not contain an existing issue key yet, the default response is instead to create a new issue, assign it an issue key, and then send out notifications that include the previous subject line, but this time it is prefixed with the issue key.
Since the first message doesn't yet have a Jira issue key, an email user replying directly to that first email message won't have an issue key either. So the logic of the email processor in Jira at this time is not smart enough to foresee this.
Since you could easily have multiple issues in Jira with the same subject/summary from different users, the behavior in this case shouldn't actually be to merge these together. You could conceivably have two different users create two separate support requests with the exact same subject/summary. To merge those requests would not be a desirable behavior here either.
I wasn't able to find any such email header with the term "reply-to-message". But in order for that or something like it to work, this email header field would have to be both unique to the first message, and then stay consistent among all the replies generated from this first message in order for this to work the way I think you are looking for here. To the best of my knowledge I don't think there is such an email header that exists, as such I believe this is why Jira is then always including the issue key in the subject line.
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