Northern Luzon will become Muslim since it is affiliated with Majapahit, before that it was affiliated with Northern Sumatra, the Majapahit affiliation is what caused the delay to Islam...
What happened is that Majapahit's destruction was 40 years before Legaspi came...so the area was mostly Hindu/Pagan..A few decades more might make it more muslim..
Highly doubt it. Even Mindanao before mass Christian settlement during the 1930s had only 70k Moros per 1918 US philippine census. This points to Lumad dominance rather than Muslim dominance like Dayak dominance in Borneo before Indonesia or Malaysia mass settled Borneo with Muslims.
If Most of the islands particularly were Muslims supposed to be strong still minorities by 20th century, how do you expect them to majority by 1500s or 1600s were Brunei/Islam control is even in question by local rebellion.
The best way to describe Islam strength in the island is like Anatolia a few decades after manzikert, rulers mostly Islam, majority population non Islam. Took centuries plus mass conversion to convert majority Anatolia into Islam. And the Moros never did that to Mindanao nor did Brunei ever did that in Borneo in otl.
Islam should be treated a new invader like the Spanish rather than an old established religion like the Hindu in the Philippines or the more ancient native religions. States like Sulu is more the exception to the rule peacefully converting to Islam.