Any obvious differences if instead of Spain it had been Portugal to conquer the Philippines?
Only in the case of the French in Rio in the 1560's. By 1640 Brazilian sugar was already the heart of the Portuguese Colonial Empire, generating more revenue than spices from Asia.Depending on the PoD, a Portuguese conquest of Phillipines might even make them less interested in Brazil (which until the late 17th Century was a backwater), and might make them decided the reconquest of a lost Brazil (say, if France or the Netherlands grab a piece of South America) is not worth the effort. This, in turn, might devolve the Portuguese into a greater exploration of Oceania... likely putting them at odds with the Dutch, and likely Spain (if it indeed has any presence in Asia whatsoever).
spain might try getting sakhalin or taiwan, philippines would be lost to the dutch.