With a POD in the early 17th century who knows if Mindanao is part of the Philippines, if such an entity exists, in ATL 2016?
But to address your question, Ternate and Tidore were both sacked by the Spaniards in 1606. The POD you outlined would mean Spain takes Fort Victoria in Ambon and terminates the alliance the VOC had arranged with the local rulers, cementing Spanish power in the Malukus. But considering Spain's 17th-century position and the issues I outlined above, their role is probably not too dissimilar from the role of the Portuguese in the early 16th century; Spanish naval power and internal Malukun division allow Manila to wield significant regional influence, but there is no spice monopoly. Malukuns retain great independence and Spanish positions are significantly more dependent on local allies than was the case OTL for the Dutch. I think only areas with a large Catholic population, like parts of Ambon (a third of the population of Ambon was Catholic), would be truly loyal to the Spaniards. And there are important challenges to the Spaniards by mid-century: Portuguese independence, Makasarese expansion eastwards, the intrusion of Western Europeans, and various vagaries of history like Koxinga.
IMO it's possible (if not the likeliest possibility) that Makasar would expel the Spaniards from the Malukus. As a major Islamic power, Makasar holds the legitimacy to unite the Muslims of the Malukus against the Christianizing Spaniards (this possibility was why the VOC banned proselytizing to Muslims).[1] And as the largest eastern Indonesian empire in history, it had the capability to take on the Spaniards and have a chance at victory. After all, an Englishman reports in 1615 that when the Sultan of Makasar made ready for war, "at an instant were mustered 36,000 able men."
Hehehe. Well, I mean the same loose category of semi-subjugated sultanates under the Spanish heel rather than the Dutch/British one. And yeah, the Portuguese going free would be a problem.
So, the Maluku islands can, in fact, be kept under Spanish rule and Christianized? Interesting.
From what I understand of the history of Mindanao, it kept on being subjugated but the subjugations kept on not sticking until the Americans and the settling of Visayan landowners via the homestead program all over the island. So really, the majority of Mindanao wasn't Christian until we were well into the 20th century. All that's needed is a loyal Christian minority.
As for Makassar, it sounds very interesting.