In Clifford Geertz' classic volume Agricultural Involution: the Processes of Ecological Change in Indonesia (1963), the author argues that the Javanese form of wet rice cultivation has a very high potential to "absorb labor". While Geertz' view has been criticized – for an enlightening discussion see Wood (2020), Chapter 6 (preview available on Google Books) – it is a good starting point towards answering your question. Wood writes:
It is fundamental to Geertz's view that different agricultural systems
have different capacities for labor absorption and involution.
According to Geertz, wet rice farming as practiced in East and
Southeast Asia probalby has the highest capacity to absorb labor of
any form of traditional agriculture...
Thus, the particular attributes of wet rice farming systems in the tropics and subtropics allow these systems to support, and indeed in the views of some authors demand, high population densities. High density, high intensity wet rice systems are found throughout south and southeastern Asia.
However, as other responders to this question remarked, the properties of the physical environment are also critical factors in the potential for a high density wet rice system. Growing season temperature and rainfall will influence potential productivity, but in tropical and temperate monsoon Asia, soil fertility is probably more important. So the best examples of high density rice systems are found not just in the young, fertile volcanic soils of Java, but also along the major river valleys and deltas of the region, e.g., Mekong, Red, Chao Phraya, Irrawaddy, Pearl, Yangtze, Ganges, and in the fertile but narrow volcanic valleys of Japan. As noted above, the other islands you mention:
Madagascar, Borneo, Sulawesi, Honshu (Japan), and Sri Lanka
are characterized by older and more complex geology with significantly less fertile soils, and in the case of Japan, substantial areas with cool to cold temperate climate where rice agriculture would have been limited to a single crop per year, if at all.