This would really vary. First off, the Philippines are a mix of Muslim and non-Muslim kingdoms, such as the Kingdom of Tondo and the Muslim Sultanates of Sulu and Maguindanao. This would probably result in Spanish colonization of about almost every Philippine island north of Maguindanao Island unless the Muslim Sultanates have a great leap in ships, military strategies and gunpowder uses. The only problem is that the way in which the Spanish fought was new and unseen to the kingdoms there, and mass-producing gunpowder and storing it in tropical South-East Asia would require some big thinking, all within just a few years of Spain's arrival.
If you want to kick-start SE-Asia into the Early Modern period and sail the Unknown Seas, then you would have to give it an enemy or a conflict that would require the kingdoms there to innovate and invent new things and thoughts first before Spanish arrival.
Actually, given the long history of Chinese and Japanese immigrants to the Philippines I wonder if a Islamic, Chinese-Japanese Sultanate in the Philippines could be established.