>if the goal was mainly trade the Spanish could have made use of Manila similar to how the Portuguese and Dutch used Malacca and Batavia during the 17th century: as trade hubs and chokepoints to control, dominate, or divert existing trade routes - without caring too much about conquering the hinterland and converting the native population

I would argue with Manila the Spanish actually kind of did both. I suppose the "conquering and converting" was the bigger and more lasting impact of course, but I thought that in some small way the galleon trade did sort of "control, dominate, or divert existing trade routes" that existed before the Spanish period.

For example, pre-Spain the Philippine kingdoms used to trade a lot more with the Malay and other Southeast Asian regions, even as far as India (and Arab regions) I guess—in addition to the existing China trade; but after Spain came in, the South/Southeast Asian trade mostly disappeared or at least is not heard of as much, compared to the new connection with Mexico/the Americas and the expanding Chinese connection, partly due to Chinese who wanted Mexican silver.

But for sure conquering and converting was always somehow much bigger for the Spanish. Somehow I feel it might be why the Filipinos got so much more culturally changed than their neighbours in SEA—but not so much physically, as few Spaniards actually went all the way there to settle, except for friars, and barring those cases that raped or otherwise knocked up native women, they wouldn't generally be able to have offspring.