Thanks to everyone for this discussion. As a regular user of (what is now) 1W96 I'm all too well aware of the havoc (and snowballing delays) which late running to Edinburgh can cause further north, so anything which helps to improve that gets my vote. This (rather than the Waverley docking issue) better explains why the Glasgow service remained an "S" and (to my mind anyway) is a much better solution than the use of the "class 9" (international) code.
I'm also grateful for the explanation of why it's 96 rather than 16 to Inverness!