According to Diamond, the major significance of the different outcomes is that they show the importance of food production. One of Diamond's major themes in the whole book is the idea that cultures that develop agriculture early have a huge advantage over those that do not. Diamond argues that the experiences of the Austronesians in Indonesia and New Guinea show this.
In Indonesia, the natives never developed agriculture and were still hunter-gatherers when the Austronesians came. Natives of New Guinea, by contrast, had agriculture and settled together in densely populated areas. Because of this, the New Guineans had technology that was as good as that of the Austronesians. They were resistant to epidemic diseases. These things helped them to resist the Austronesian incursions.
So, the different outcomes were significant because they show how important it is to develop agriculture sooner rather than later.