There has been a lasting movement of resistance against the Indonesian Army in the Western part of New Guinea, since Indonesia took it forcibly in the 1960's. This fact is aknowledged in the article. However, the current status of East Timor is not correctly expressed in National Geographic's Map, as you can see in this image. According to the United Nations, East Timor is not part of Indonesia, being a Territory under Portuguese administration, its Decolonization Process having been brutally interrupted in 1975.
A much more accurate information was given twenty years ago in National Geographic's issue of November 1975, (ironically just a few weeks before Indonesia invaded East Timor). You may check the differences on that year's map...
Please notice that this one is still the correct representation of the political boundaries in this part of the Asian-Pacific region.
If you wish, you can send your comment to National Geographic Magazine:
National Geographic Magazine
Washington DC 20013-7448