Your first point isn't exactly true for the rails relevant to the article. Outside some mining railways, the track is owned by the Australian federal government, like the roads. I don't know how the usage fees and tax structures compare between the two modes.
With regards to your second point, it depends on the cargo as to whether that matters. A lot of the cargo will also travel by ship for some of its journey, and that will take a lot more time, so the land side journey time doesn't really matter.
Autonomous pod bullshit doesn't help here. One of the major advantages of rail freight is the economies of scale. You load up a big efficient train full of stuff because you have so much stuff heading in one direction.
The article actually has a quote that sums up the why:
"It's largely due to the inefficiencies of a fragmented national rail network, ailing infrastructure and government policy and investment that favours road over rail."
The answer is just to invest in rail and incentivise its use.