Someone will need to have a serious talking to to QR, the Port of Brisbane and Aurizon though, as rail at the Port is not set up for taking much in the way of containers; 95% of container movements are by road. You are lucky to see more than one container train go there per week. Aurizon have a small container transhipment yard in the centre of Fisherman's Island, PN, Qube etcetra are shut out of there at the moment. The yard is between the major ring road with no unimpeded access to each of the stevedore company's dockside and there is no loading facility for vehicles. The major traffic is coal and will be for years, even after the inland railway is finished.
Open to correction on all that follows (i.e. I'm very possibly completely wrong).
I think the "small container transhipment yard" you refer to is actually the Brisbane Multimodal Terminal
(BMT), which is operated by the port itself as a common user style facility. If rail operators other than Aurison are not using it then that's because they don't have sufficient custom for that service, rather than being shut out. I think state and federal competition bodies would get very excited very quickly if one particular rail operator was able to exclude other operators from such a facility.
That terminal effectively has reasonable access to all the port related facilities via the port road network. A large number of containers are already shuffled around between sites at the port (perhaps by conditionally registered vehicles) on that road network. The logic of having one single rail terminal rather than service to each facility is that you get economies of scale with your trains, at perhaps the cost of some re-handling at the port. The terminal can also be easily used by industries that are located over that side of Brisbane to load containers onto trains.
The market share of rail then probably reflects more where the containers are going (mostly local deliveries to south east Queensland), rather than port infrastructure limits.
I don't think this is all that relevant for the inland rail anyway, because, again just my understanding, land bridging wouldn't happen to any great extent with the distance between Melbourne and Brisbane. If you are overseas and you want to send a container to Brisbane, you put it on a ship to Brisbane, while if you want to send it to Melbourne, you put it on a ship to Melbourne (it might be the same ship, doing a milk run down the east coast of Australia). If there's no direct shipping service from origin to destination, then the container would more likely be transhipped at one of the big shipping ports (Singapore, Hong Kong, etc) onto an appropriate ship.
Aspects of this inland route strike me as "giving up" on the coastal corridor and the Sydney-xxx services. I'm not sure that's a good thing, but the problem is that fixing Sydney (particularly to the north) is expensive, and fixing the rest of the northern half of the coastal route isn't cheap either. For example, I know BDA likes the Fassifern-Stroud Road link, but that doesn't make it into the list of upgrade projects for the coastal corridor until someone volunteers well over $3 billion of extra investment for the corridor (spend on the entire Melbourne - Sydney bit, not just the short north). The sequence that the various upgrade projects are selected is interesting - see the North-South corridor study for details.
(Some of that $3 billion might have already been spent with the recent Victorian resleepering works, not sure.)