Am I right in thinking that there is no way to change what gets put in the subject line of a mailbox email auto reply?
No, you are not right! You can modify this in Admin->Mailboxes, the auto reply template.
Forgive my ignorance but I definitely cannot see a way of changing the subject line of the email auto reply:
There is a subject line textbox to all the other templates on that page, just not the auto-reply!
Doh, misread. James you are right!
All the system does is give it a RE then uses their subject and adds the ID. You cannot currently modify that behavior.