Much the same way you calculate the full economic price of a maintained road to every possible place. You don't and pretend the cost of driving is just the car and fuel.
Trains become economic on the shear scale of use, when you realise that during peak each train is shoveling 1000+ commuters around the city at a rate of one every few minutes or less. It will be a very long time before planes or cars can produce similar results.
The new HC Metro trains will carry up to 2000 per set. That's about 1000 cars off the road per train assuming an average of 2 per car. Apply that to a properly set up city pair like Melbourne - Sydney and resonable travle time like 2 hours where you are in commuter range, the scale will be there. It's just a matter of initial capital to build it.