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From what I learned, the only reason why it did not happen is that Lowland Northern Luzon converted to Islam in early 1500s before the Portuguese would be able to convert and colonize them - Muslim scholars and historians know this fact, the second POD for this is actually the Maniago revolt succeeding and the Spanish are forced to cede Northern Luzon to Portugal in the Independence wars, saving their ass from humiliation.
We would focus on the first POD, If Portugal successfully convinces the people of Northern Luzon to bow to Portugal, would Portugal also colonize the rest of the Philippines?