I don't think this is what you're going for, but i had this idea a while ago and never developed it.
My idea for Portugese settlement of Australia would be a ship bound for Timor is wrecked close to the northern Austalian coast, so most of the crew survives. They're discovered about ten years later, by that time most of them have married. A dozen or so of these ship-wrecked sailors decide to stay and start plantations, enough to get a ship or two a year to stop in and sell supplies. When Christianity gets banned in Japan, many escape and end up in Australia (cheap farm labor?), and when the Jesuits are suppressed many of them come too. In the whole, this colony would be small and agrarian with strong religious tendancies. Due to bored Jesuits, i would expect a good (possibly excellent) university in the main port town and proselitization among the Aborigines, maybe even a system of missions.
Questions i have about this, is there gold to find, any native plants that would be profitable to export, can tea or spices grow well in N Australia? Naturally, discovery of gold or large tea/spice plantations would really change things, but i think the above is a good start.