The possibility of Spain not being able to conquer Luzon or for the island to fall under the same historical and political limbo as Bangsamoro (not including rest of Mindanao, of course) is if there was rapid Islamization of at least the Manila area. This situation would be akin to what Muslim history around Bangsamoro (or Sultanate of Sulu) as they could have also fended Spanish conquest for the next hundred years or so. However, the population and political will of this region might not be very easy to compare to that of its hypothetical southern brother of faith. The Muslim society of Bangsamoro could have still been way more intact than that of the territories of the House of Allah (Bolkiah). Aside from the fact that if this area of the island could reject Spanish influence, the fate of the entire Luzon might be blurry since the rest -- particularly the Kapampangans northwards -- could have been still Christianized since they were predominantly Hindu-Buddhist-animist. We can see that a different economic and political center would be established by Spain around a different area possibly in present-day Pampanga or a coastal region (present-day Batangas or Quezon province) facing southwards because it could have been the most convenient en route for them from the Visayas to Luzon with the hopes of conquering that side as well.
Chinese or Japanese influence might still be blurry. The only Islamic society in prehispanic Philippines was the only prominent nation that was able to repel Spanish encroachment because their dogma and system is strictly tied to the Koran. Whereas for the rest (especially most Visayans) who are Hindu-Buddhist, their precepts and philosophy are fluid and have always been syncretic from the beginning (welcoming strong animistic influences). With this open-ended philosophical-cultural system, new influences have been easily injected by the Spanish, thus, the pervading Catholic-Christian culture that we distinctively possess apart from any other similar religious denomination in the other parts of the world. Our Catholic traditions today are very Hindu-animistic in nature such as the rationalization of saints with the anitos, the angels to the diwata, religious icons from anting-anting and agimat, etc etc.
A Spanish East Indies without Luzon would surely be a more ethnoculturally and even politically balkanized than what we could have been hundreds of years before. What were Aguinaldo or Bonifacio in OTL could have been historically insignificant figures or probably could have never been born. This would then prevent from Aguinaldo (or any figure we know in history for that matter) leading the final chapters of Luzon theater of the Katipunan revolution. There could have been no Pact of Biak na Bato or any scenario of Spanish surrender unless a seemingly parallel situation could have happened in that hypothetical alternative economic-political center. Thus, there would have also been no trips for Aguinaldo to Hong Kong and no communication with Commodore George Dewey which actually accentuated his interest in the resources and territorial benefits of present-day Philippines. But then, Spain and US were already at war there and any territorial reach of the former is a prize for the Americans if they were able to snatch it. It could still be highly possible that the American armada would still reach downwards from Canton. For one, Bonifacio was actually partly Kapampangan and much of Katipunan (as how Tondo back then) was Kapampangan. It would still be improbable that he was born as he has a Tagalog half. Either he would be born or living in any region outside Manila or never to exist at all. Still, the possibility of him as a figure in this part of history is shaky.
The rest of Christianized indies (rest of Luzon except Greater Manila Area & Cordillera, Visayas and unislamized Mindanao) would have still been the primary areas of interest for the Americans. It is uncertain, though, what would become of Islamized areas of Manila region if they would soon fully integrate or conduct the same resistance as what Muslim Mindanao has been doing ever since Spanish arrival.
Another scenario given that there was no America-Aguinaldo conniving would be easy reach for German or even British and French colonization within the Christianized areas. The Islamic territories could have also been included but may in fact enjoy the same status as what the Malay states had if the Brits or the French did arrive before the Americans could. As such, there would possibly be a fierce political and/or military tension within these islands given that many Western powers, thirsty for strategic control over Pacific, would scramble for Spanish spoils. In short, Northern Luzon, Bicolandia, Visayas and Mindanao could have been solely German, British, American or French territories subsequent to that of the Spanish OR the islands would again be politically fragmented and dissected by these colonial powers to avoid imminent war. I suppose much of Luzon would be American or German while Visayas and Mindanao would be British or French.
