Hi there, could you maybe expand on what you mean by "primate" cities? I assume you don't mean cities populated by apes :-)

I cannot speak with regards to the other SE Asian cities, but I can speak with specific regards to Manila.

The population of Manila - or more specifically Metro Manila which includes several other outlying cities and municipalities (that all arguably form one mega-city) - increased greatly in the post-WW2 period primarily due to the centralization of resources and infrastructure development in this area.

Part of the reason is the fact that Manila was the center of international trade in the Philippines - it has the country's largest international port and airport. As an extension of this Manila, or more specifically the business districts of Makati and Ortigas, ended up housing the local headquarters of various corporations. On top of all this was a concentration of government agencies - all of which were essentially headquartered in Metro Manila (e.g. the Supreme Court, the Congress and Senate, etc)

As a result there was a fairly extensive migration from the rural areas to Metro Manila, similar to what was seen during the industrial revolution in Europe, which resulted in the creation of large shanty towns composed of the migrant poor that comprise much of the population (and were encouraged to remain in Metro Manila despite their poverty to serve as a voting block for local politicians).

Eventual economic development however slowly reduced the shanty towns (albeit many still remain), while commercial and residential development increased to house and serve the growing middle class. This resulted in an increasing population density in Metro Manila (some municipalities are now more densely populated than Mumbai), and the absorption of some nearby provincial areas into the city proper. The city of Pasig - which is the eastern portion of Metro Manila - for instance was originally part of the "rural" province of Rizal but was absorbed into the growing metropolis. Further south, the province of Cavite has become so populated by residents working in Metro Manila that it has practically become a suburb of the metropolis.

Hence, to summarize, the size difference was caused by the centralization of government institutions and investments. This caused a migration of population from rural areas to the city, which in turn caused the population and boundaries of the city to expand.

That said it is now being recognized that there are massive pitfalls to this approach - as evidenced by the aforementioned massive population density and the worsening traffic situation. This is why there has been comparatively more attention, if not investment, made in other cities such as Cebu; albeit the disparities you noted still remain rather extreme.