There seems to be a deep and ancient connection between the populations of Southeast and South Asia, most evident in the substrate of the Cambodians. In First Farmers the author relays an early report about a farming community in northern Vietnam where morphological and ancient DNA evidence both pointed to a stabilized coexistence between a classically East Asian majority population and another which he terms “Austro-Melanesian.” This latter group has been predominantly absorbed today, but seems to persist in isolated tribes such as the Senoi. But these are most certainly residual elements, near extinction, and it seems the dominant genetic heritage of major ethnicities such as the Khmer derives from agriculturalists who left southern China over 4,000 years ago. Only in eastern Indonesia does the Melanesian component of ancestry in Southeast Asia begin to increase to a non-trivial component, and this area is truly as much or more part of Oceania than maritime Southeast Asia.
The Indian subcontinent has also characterized by a synthesis between outsiders, who likely brought farming technologies, and the native inhabitants. These ancient populations had very distant connections to the ancestors of the hunter-gatherers of the Andaman Islands, and no doubt with the peoples of pre-agricultural Southeast Asia, and further on toward Oceania. This is not to say that the zone between the South China Sea and Indus was homogeneous. Rather, like Northeast and Northwest Eurasia, it was likely a region where peoples diversified from an original Pleistocene element which arrived ~50,000 years ago, and retained broad affinities through gene flow and common ancestry. But whereas the farmers in Southeast Asia came from the north, those in India came from the west. Additionally, it seems clear that the fraction of ‘indigenous’ ancestry is far higher in South Asia, on the order of ~50% across the subcontinent. The equivalent figure for Austronesians, Daic, Burman, and Austro-Asiatic populations of Southeast Asia of Pleistocene hunter-gatherer is probably closer to ~10% (higher in the Austro-Asiatic, least among the Daic).
So I have decided to offer up a hypothesis: the agricultural toolkit which West Asian farmers brought to the northwest fringe of the Indian subcontinent was far more constrained in its ability to expand than the equivalent for the rice farmers from southern China. Though there is still debate, it seems that the dominant Indian cultivar of rice has an East Asian origin. Though wheat plays an important role in Pakistan and northwest India, rice is the staple crop for the preponderance of the South Asian population. Though I hold to the proposition that the Austro-Asiatic populations of South Asia are recently intrusive (i.e., they are not the primal inhabitants as some would argue), for geographic reasons, it seems that east to west migration across the difficult north-south mountains separating South and Southeast Asia served as a check on migration from farmers in that zone. Ultimately it was South Asian rice farmers, a hybrid population, that pushed south and east and absorbed the tribal hunter-gatherers who remained in their fastness (the current Indian tribes are not descendants of the original hunter-gatherers, but admixed populations at the margins of Sanskritic civilization; both genetics and their mode of production suggest this). The long pause in the northwest due to the limitations of their agricultural toolkit may explain the difference between South and Southeast Asia in the completeness of their demographic assimilation. Where the rice farmers from southern China swept across all of Southeast Asia rapidly in a singular sweep, the West Asian farmers were halted for many generations at the limits of their ecological range, absorbing genes from the hunter-gatherers on their frontiers. The analogy here would be the Xhosa, Bantus at the edge of their range of expansion which have absorbed a great deal of genetic material (~25% of their ancestry) from Khoisan populations. Once the proto-Indians of the northwest had accumulated enough cultural adaptations their distinctive West Asian genetic signal may already have been substantially diluted by gene flow from the hunter-gatherers to the south and east. The subsequent expansion into the forest zones was likely a demographic disaster for the old natives, but the newcomers themselves were already partly cousins.