Continental drift occurs over millions of years, by contrast indigenous Australians arrived approximately 65,000 years ago, so the difference in land masses would have been negligible over that span of time.
As other posters have said, at the time sea levels were lower, and while there would have been land bridges connecting PNG to Australia and Java, Sumatra & Borneo to SE Asia, journey by boat would still have been necessary, although the journeys would have been shorter than those required today.
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