Perhaps you don't understand the TOC Manual, it lists locomotives by type/class as a reference, it does not list every item on the network. Sure some are listed individually but that's more I would suggest because history of what was correct in 1969 is now forgotten.

If they were listing vehicles by actual number then we would see the 5th digit check number as well would we not?

A look at THNSW in the John Holland TOC Manaul doesn't even show the correct business name from the change 12 months ago so while a reference manual it isn't perfect.

ss

1: I understand it perfectly, it does not list them as a reference, it lists them when they are authorised to run on each of the 3 networks.If they are not in the TOC Manual then the only way they can run is on a TOC Waiver. It also tells staff the operating restrictions on each vehicle eg whether they are block workers or speed restrictions, weight ,length etc.
2: Unfortunately they do list every item that can run on the network and it has nothing to do with history.
3: No. I would suggest a more thorough reading of this section. In most cases, it is only the classes that have large members of that class that do not list all numbers.
4: I can find Sydney Trains and NSW Trains locos and rolling stock under their owners names and yes it has to be totally correct.
(Section 10 Locomotive and Rolling Stock Data)