You may refer to my previous answers here, here and here.

You are correct in that Spanish miscegenation in the Philippines was overstated; and in fact the majority of the prominent Filipino families today considered "mestizo"are not mixed-Spanish but in fact mixed-Chinese. That being said, an assumption to get out of the way is that Filipino surnames are in any way a clear indication of ethnicity. Some Chinese immigrants chose new Spanish names as part of their conversion to Catholicism (e.g. Lam Co to Domingo Mercado), or simply concatenated their Chinese names to comply with Spanish laws (e.g. Cojuangco, Lichauco).

What many people overlook in studying Philippine society is the sheer influence of mainland China that was on par if not even more consistent than the Spanish and American occupations. Chinese traders had an appreciable presence in the Philippines centuries before Spanish contact, and many of the earliest written records of precolonial Philippine society were from Chinese sources. When the Spanish arrived in the archipelago, Chinese traders and artisans made for a very convenient vibrant middle class whose presence could be relatively easily controlled via immigration decrees, conversions, massacres, etc. These roles were quite important especially in the face of a severely underdeveloped colonial economy.

Before the 1800s, the most important city in the Philippines was Manila by sheer virtue of its location as a port city for the Manila-Acapulco galleons, which transported silver from the American colonies in exchange for Chinese goods. The rest of the country in comparison was relatively ignored in terms of economic gain and/or resource extraction due to in no small part of the remoteness of the colony. This meant that the Philippines' expenses had to be routinely propped up with a subsidy or real situado from the Viceroyalty of New Spain. So during this time, the relatively tiny Spanish population was mostly confined to the walled city of Intramuros and other sparse urban centers and garrisons throughout the archipelago, followed by the Chinese and then the rest of the indio masses that were mostly ministered to and governed by the Spanish friars in the provinces. The friars, who were mostly the only Spaniards willing to live so far from the cities, were aided in their responsibilities of governance by the so-called principalia, or the native elite that were coopted as intermediaries between the native population and the Spanish colonizers. However, these classes were not yet to become the full picture of the modern Filipino elite.

This state of affairs began to be shaken up in the late 18th century when the Manila galleons started losing money due to the expansion of British maritime power in Asia and of course the later independence of the Spanish American colonies. Because of this, Spanish administrators were forced to consider the Philippines' other economic prospects particularly in terms of natural resources. During the early 19th century, ports throughout the Philippines were gradually opened up to international trade, which included amongst many other things Chinese immigrants and British trading houses that provided entrepreneurs and capital for a burgeoning cash crop industry for sugar, copra, tobacco, etc. This expanded the economic potential of Chinese immigrants all throughout the country, who were able to own more land and intermarry with the principalia in order to become political elites in their own right and a challenge to friar power in the provinces.

Modern Filipino oligarch clans like the Lopezes, Cojuangcos and Ongpins, as well as the leadership of reformist and revolutionary movements like Jose Rizal and Emilio Aguinaldo, were the precise results of this social phenomenon in the mid-19th century. They came to clash with the friars in terms of land ownership as well as intellectual and spiritual conflict in terms of the inherent "dignity" of Filipinos in relation to Spaniards, which would become the catalysts of the 1896 revolution against Spain.

The American invasion and occupation, though, would be the final factor in the consolidation of these elites into a national oligarchy. Treaties like the Tydings-McDuffie act and the Hare-Hawes-Cutting act guaranteed import quotas of purchased cash crops to the USA in return for continued Filipino collaboration with the American colonial state, meaning that the Filipino agricultural elite would be firmly entrenched within their dominant economic and political positions for years to come. Secondly, the American administration served to create a national apparatus for political authority with the Philippine Assembly and the eventual Commonwealth in 1935, opening up new opportunities for local elites to gain access to the resources of the entire Philippine state, partially resulting in the current state of "musical chairs" of the Manila government in terms of the ever-present oligarch clans feuding over booty and plunder of the national treasury.