AFAIK the sidings within the yard were effectively level.
Referring to the the picture posted, the train is on the run-around loop and this view is looking north (towards Brighton). Access to the yard was at the north end of the loop, beyond the loco, probably just off this picture. There was a headshunt, and sidings came back parallel to the main line and run-round loops shown here. They are (were) situated just behind that row of trees on the left side of picture.
I believe there were about 4 parallel sidings in the yard (behind those trees), serviced by pumping hardware for filling the tank wagons with the various petrochemicals. The sidings didn't extend any further south than the point where this photo was taken and didn't go into the main part of the refinery.
The photo was taken from a pedestrian footbridge at the far western end of Sherriffs Rd, Lonsdale and is easily accessible, either by car or from Lonsdale Station. Today you will still see the two run-round loops, now surrounded by electrified fence & floodlights. Used by TA to stable jumbos & 3000 railcars overnight (plus a couple of railcars in the mid-day siesta, when Noarlunga service is cut from 15 to 30 min freq.) No freight, unfortunately, and the Chrysler/Mitsubishi sidings on right-hand side of photo are truncated, rusted and overgrown, but at least some track still there.
The "Port" in Port Stanvac Yard is a bit misleading, as it is a long way, both vertically and horizontally, from the sea. The actual Port Stanvac was used mainly to offload crude oil for the refinery. There is a jetty, but in recent times I think ships "park" (or whatever it is that ships do) a long way offshore against a buoy and connect to an undersea pipeline. They pumped the oil from the ships this way, which has caused a spill or two in the past. There is no public access to this "Port" and no real need for the railway to go down to the sea.