There's so much wrong in these two sentences that it just seems...so right.
Serious note though, it'll probably be some combination of random sultanates, the Dutch, or Portuguese.
China's had a tendency of having a massive overseas presence due to migrants while also completely ignoring said migrants. So while there almost certainly will be Chinese Han presence (in OTL, there's quite a few Filipinos with Han ancestry), it probably won't be state sponsored (just going by OTL trends).
Japan's even less likely as their main focus has always ever been the mainland, i.e. the Korean peninsula and China. A victorious Toyotomi Japan that conquers AND maintains long term control of the Korean peninsula (which is unlikely seeing how much trouble they had doing the former despite having the element of surprise and more more-experienced troops) will be dedicating most of its resources projecting into China and Manchuria, then also defending from northern nomads, for at least the better part of a century. By which point some European probably has a stake in the Philippines or the Japanese turn their attention to solidifying control of SE Asia (and going bankrupt in the process since that kinda happened with most of the Chinese dynasties at some point, attacking Vietnam and suffering terrible financial losses) or the north. The Southern islands just don't have the same appeal prestige or financially that projecting towards the mainland does, especially for a nation in the Sinosphere, and controlling China as a foreign invader forces quite a bit attention towards bureaucracy (especially if the capital of Toyotomi Japan is not Beijing like with the Jin, Yuan, Ming, and Qing, forcing a shift in management), rebellions, and raids.
China is probably the next-most likely, and i'm not just saying that because of their proximity: iirc, for a time the Philippines were/could have been controlled by Chinese pirates (i learned about this in a book on travel legends and folklore, been meaning to look closer into it) which were set against the government of the time, so you could probably easily justify a settlement of the Phillipines by Chinese like how Madagascar was/could be settled by Europeans via Libertatia, which in turn could mean that eventually the pirates are defeated by the Chinese government which then takes an interest in the Philippines or at least has nominal control over them and so when the Europeans arrive they find that the Chinese have already set up shop and go for trade instead of colonization
The thing is IOTL before the Spanish came the Philippines is already in process of colonization by Bruneians.