I went on a tour of St James in 1998 with the ARHS. We went out both ends of the concourse. The tunnel to the north ends in 'St James' Lake' where it dips down and heads towards Circular Quay. It becomes submerged. The tunnel to the South goes all the way to the start of Oxford Street. The concourse which is shown in the video hasn't changed since I saw it, but it isn't 'fill': it is actually a suspended floor and you can see all the way under it from both ends.
If the middle track area was only covered over in the '90s, I must have seen it loads of times. My mum was forever taking me to David Jones and we'd use St James...but sadly I have no recollection of ever seeing that area. I wish I'd being paying attention.
Back in 2001 I did a tour of the tunnels heading towards the Quay. There were public tours but either ohs or terrorist scares the tours stopped. Not sure when
St James and Museum are beautiful stations. Shame St James never really got completed, but yeah. Also goes to show how they used to plan and build ahead of time .. Not so much a thing these days.
For a little bit of history my mum work for Marcus Clarke now the tafe building in railway square as a telephone operator during the war years their room over looked the goods line as the train came out of the tunnel blowing there whistle loaded with troops going to war the girls stop work race to the windows and wave goodbye to them after work mum would go to St James's station escorted down one of the tunnels by a air raid warden to operate the switch board for war effort off Northern Australia
BR did experiment with double deckers with the SR class 4DD from 1949 to 1971. They were a failure because they took too long to empty out and refill. Sydney's railways are still grappling with this lesson, but due to widespread restrictions on train lengths (the UK Southern increased from 8 to 10 to solve the problem), Sydney railways are stuck with double deckers because they can't increase platform lengths. Fortunately, when the new North West Metro was built in Sydney, they adopted modern practice of single deck with multiple side doors like London's underground and Hong Kong's MTR. These are purpose built for rapid transit and rapid empty and refill. Hong Kong's MTR was involved in the Sydney Metro.