Settlers from southeast Asia would have a limited amount of land in Australia that would be useful to them. According to
@Jared as well as Jared Diamond, outside of the northeastern coast of Queensland there isn't really good growing land for southeast Asian crops. So the Aborigines would not be taken over, at least at that point, and most would remain hunter-gatherers even if their cultures do creole-ize. Some might adopt livestock like pigs and goats, but honestly it would probably make more sense to the Aborigines to adopt bows and arrows and hunt these animals after letting them go feral than change their lifestyle so drastically to become ranchers. New Guinea might see more Austronesian settlement (than OTL, anyway) but this would be concentrated in the western peninsula, with the highlanders and sago swamp people largely left alone.
Now I'm avoiding the how this happens because it's not in your question, but suffice to say this would require some pretty massive changes in trading networks in maritime Southeast Asia to happen.