The problem with colonization is Southeast Asia is mostly malarial in the lowlands, which means until the 19th century Europeans had a nasty habit of getting sick and dying. Even once you go through it and survive, and are hence immune, your children will also get malaria and tend to die in large numbers, which could potentially mean a negative birth rate among European settlers.
In general, highlands are a better idea in terms of European settlement in tropical climates. However, the highlands in Southeast Asia aren't well suited for this, as in many cases they are far in from the coastline, and in areas even the native states never fully subjugated. Not to mention they're full of people already.
If I was going to suggest one place for Europeans to settle successfully in Southeast Asia, it would be the Barisan Mountains in Sumatra. Many of them are high enough altitude that the climate is more healthful. And they're not that far away from the coast as the crow flies. Still, the upland areas are dense, undeveloped subtropical rainforest, and it would be tough going to clear out the forest land and develop real settlements there.