I'm not sure I agree with the authors take on the unfairness to the greens here. The greener electorates manage to elect green MPs. In the seats where they are close, the preferential voting system works as intended. The conservatives can say hey I want the libs in but if they don't make it I would rather labour over the greens.
How else should it be done? As far as I can see switching to a first past the post system would be significantly worse.
People in the minority of their electorate will always feel a bit salty about the outcome, but that's unsolvable. Having the senate mitigates this already in my opinion, where the greens have roughly proportional representation. There is perhaps an argument to make the senate pool federal rather than state and territory based (looking at you Tasmania).
Moving the lower house to a federal type pool would remove any chance of area localised representation. Not that our current system is great at that with most MPs only caring about the party line, but at last some electorates have members that care about local issues.