Australia never was an empire, and it might never become one(thou no one of us is to know what the future brings). And Eu4 is more or less historical game. Also EU4 have whole world included. It is not like CKII, when you don't know what happens in the ROTW. Things are happening in asia and americas. Australia back in 1444, was just bunch of wildmen, realy sparesly populated, place. Propably whole population of australia in 1444 was lower than population of small european city. Even right now, poland have bigger population than australia. Aborigens invading europe, is much more fantasy, than aztec invasion(at least aztecs had the numbers that would allow them to do something like this).
In australia, there are about fife hundred thousands(at least wiki says so on site about australia) of aborigens right now. Quite big population imo, considering australia is just a big desert island, with only habitable places being on shore.
More plausible would be chinese invasion.