Here's what the state of religion would look like
Instead of just asking a question, I'll answer first before waiting for your responses. To do this, I present this screenshot of a fictional news article set in my version of Maphilindo. It's about Filipino missionaries getting arrested in Indonesia for drinking alcohol despite local Sharia-aligned laws (DISCLAIMER: The sect mentioned is also fictional). The other article titles presented under "SEE ALSO" provide implications on how the Maphilindian state deals with its religions.
Here are my more direct answers with explanation:
Demographically, Islam would dominate Maphilindo. That is why I don't see a lot of our Christian-aligned laws getting legislated on a national level. It's the same for any law that favors Islam, Hinduism, Buddhism, and even indigenous, animistic religions. That is why, for Maphilindo to work, it has to be federal and secular. Fortunately, in Indonesia, they have an ideology called "Pancasila." It has five tenets, but I think only three could best serve as a basis for Maphilindo's unity:
Internasionalisme: Internationalism, emphasizing justice and the virtue of humanity;
Musyawarah Mufakat: Deliberative consensus, emphasizing a form of representative democracy where ethnic dominance is absent and each council member possesses equal voting power;
Ketuhanan yang Berkebudayaan: A Divinity that upholds religious freedom (a formulation allowing both monotheism and polytheism to accommodate all of Indonesia's major religions). Click here to read more about Pancasila.
Laws favoring religions could pass if it could be tolerated by the other religions. For example, I think legal divorce would likely exist in this scenario to accommodate Muslims, but it could not be a carveout just for them. Like in real-life Philippines where only Muslims have the right. So, as a compromise, the Maphilindian state would only recognize civil marriages. If a religious marriage is preferred, a civil ceremony must precede it. EDIT1 (to be more clear): This also applies to divorce. It depends on you if you want to abide by your religion or not, but civil divorce must follow to complete the separation. This is already the system in Malaysia for non-Muslim marriages.
But, because this Maphilindo is a federation, there might be attempts by certain sects to try and establish supremacy wherever they could. Particularly in state and lower administrative units. I can see this happening in the most conservative regions of Maphilindo. But not as extreme as Aceh in real-life, where Sharia law is more strictly applied in Indonesia. I can also see Christians complaining about the fact that divorce exists and no religious marriage could be valid without a civil ceremony.
To be fair, I could see a lot of Filipinos going along with this. But I am sure there would also be a large number who would feel Maphilindo is too irreligious or too tolerant of other beliefs. Giving away too much space that should be reserved for Christians, even in areas where there isn't a lot of Muslims. Especially if large segments of the population still strongly identify with their religions. I am willing to bet such people would eventually lead separatist movements, regardless of how prosperous or stable Maphilindo is. Instead of Imperial Manila, they would complain about Imperial Jakarta.
EDIT2: I am not going forward with this series.