In the GGS book, the NS orientation is appointed as only one of the reasons that Eurasia was more developed than America and Sub-Saharan Africa. It also considers narrow points and bottlenecks (e.g., panama) which hampers migration and technology spread; the fact that American corn was less efficient in calories-hour than Chinese rice or Eurasian wheat; diseases and immunology; existence of suitable domesticable animals for cargo and work; and some other factors.
So, considering only one factor is already a weak argument.
Besides that, the NS orientation only hampers technological spread if the climate differences are large. We should ask if primitive solutions in agriculture, societal organization, health, transportation, communication, weather forecast, food storage, etc, that work in one area, still work in the other area.
Egypt/Sudan (river surrounded by desert for some thousand km): I guess if something works in Low Egypt it is still more or less valid in High Egypt, at least when close to the Nile. So this argument is not applicable in Egypt.
Africa: The coast of Magreb is much more amenable to agriculture and civilization than the Sahara. Then Sub-Saharan Africa is tropical (tropical diseases, heavy rain, heat, different fauna and flora), very different from Magreb. Going south you have deserts again, in namibia, and an almost temperate climate in South Africa tip. I guess that a primitive tribe or city-state from Tunisia would not easily thrive if teleported to Congo.
So we can apply the argument to Africa, although not as strong as in America.
For an island, it would need a very large island for the argument to start to make sense.
A primitive tribe from Aceh (north Summatra), if teleported to Eastern Java, would still be able to farm with similar techniques? Still have access to the same kind of pack animals? Similar natural resources? Similar diseases? I guess these are not extremely different climates.
Besides that, the argument is not so valid anymore after faster transportation, large scale commerce, education, large countries. It was not so valid even in colonial times. The book deals with the emergence of civilizations, not with comparing current developments.
If the NS-orientation argument is valid for Java/Sumatra, then North Sumatra should have been already less developed than Java 1000 years ago, well before the dutch and muslims!
Did the muslims or the Dutch helped Java in some way to overcome Sumatra?
I guess, for example, that Java was more important in spice trade than Sumatra, since the most famous spice islands are east of Java. Besides that, the dutch capital was in Java, this should help development.