I have travelled Spain to/from Portugal on public transport several times over the past few years and have never been asked for my passport or any other documentation.
I doubt that Portugal will take a unilateral stance re-Australians without concurrence with the other Schengen agreement countries. If Portugal is your point of entry to the EU, they may require that you have a return ticket (out of EU) on your arrival (as Ireland sometimes does). They can do that within the current guidelines.