I think that what you are probably seeing at this relatively recent date are the mixing of several different populations. You have the Negrito /Lawa, Southern Chinese and Malay characteristics combined. Perhaps some Mon or South Asian as well. Culturally, you have the beginning of Indianization to the west and the Chinese from the north meeting the Hua Dong (Sp?) and Ban Chiang indigenous groups. There is little evidence of massive population movements or extinctions, so one would gather that relatively small groups from outside intermingled with the locals.
By this time, the mix with Homo Erectus would have been well in the past with the Flores Island being one of the last points of contact. You have monsoonal forests in the area referenced by the article, so there was a greater freedom of movement. That plus the rivers carrying a majority of the traffic through well directed and traveled waterways would confirm that the society was well developed.
"By this time, the mix with Homo Erectus would have been well in the past with the Flores Island being one of the last points of contact." According to the natives on Flores, the 'Hobbits' were still around 300 years ago...and, I saw a program that speculated some may still be 'hiding' in the jungles.
But, I expect you are correct
Oppenheimer says these people in Malayasia, Orang Asli, have some of the oldest DNA in the world.