Hi Lucas,
I've conferred with some other folks and we agree that it is acceptable to break the rules for this kind of Table of Contents.
On your Transcriber's Notes page, include a statement that you are changing the format of the ToC. Instead of doing alphabetical, as in print, I would follow the order in which they fall in each volume. Then only include what appears in each subsequent volume in that volume's particular ToC.
Hope that helps!
Kathleen