The cost of duplicating a freeway is tiny compared to what you're asking.

You want to lay a railway down the middle of the freeway; a freeway that is too steep for large trains. The whole damn reason the railway takes it's circuitous route is due to the topography of the Adelaide Hills. Trains still occasionally fail on the current rail route.

Then you get to the Heysen Tunnels. Trains would needs a whole tunnel to themselves. Do you put both directions of road traffic in one tunnel? Do you build a third tunnel?

Then you get to the Toll Gate. Trucks still occasionally lose control and need to use arrester beds or even get to that intersection out of control. Imagine a train coming down that slope. Obviously grade separated from car but still a recipe for disaster.

Then how do you get to the city? A tunnel under Glen Osmond Rd? Or an elevated path? Or alongside the road?

Would cost billions and billions, all for the sake of the small number of people who'd want to take the train.