i thought the voice of the caller was a girl

I think she went to meet someone who abducted her and sold her to a brothel.

I agree with phelpsg1

The ending seemed clear enough: she went off in a car with somebody she had been having an affair with on Facebook or some similar site. The parents deny that she was on social sites, but clearly they were clueless. Perhaps they drove to Melbourne where she had a few weeks or months of fun, then returned home sadder but wiser.

I think
the brain damaged man\boy is the one she got in the car with. Tommy could not really tell as it was too dark. How he ended up in the desert for a week or however long is another unanswered question as he did not indicate he got in the car with them.
I think she was taken
and killed so that no one else could be with her and she would then be forever his. And or he being slow in mind perhaps believed some old Aboriginal superstition about sacrificing ones they love to perpetuate something or other. I surmise this from the grandmother who knew all the old customs and made a reference to "First the white one, then the black one it is the land." This also suggests Lily was not the first. But no mention of anyone else or any specifics.

Dunzo

I think she died.