Very interesting. I have been lurking for a long time, so I know that the possibility of a Japanese Filipines has been discussed many times in this forum; this are a few threads on-topic for anyone who feeks like doing a bit of reading:
https://www.alternatehistory.com/forum/threads/a-japanese-philippines.387724/
https://www.alternatehistory.com/forum/threads/ahc-japanese-spanish-war-over-the-philippines.278627/
https://www.alternatehistory.com/fo...the-philippines-does-europe-intervene.347275/
This hipothetical conflict would occur not too long after the sino-japanese war, so maybe you can have less bloodied Japanese navy leading to a more risk-taking Japan as a POD. I'm pretty sure Japan could beat Spain either way, but they can't take chances with their preciuos navy, being an island nation and all that. The most obvious choice for a conflict starter is the 1896 incident where a Japanese ship was retained at por in Manilla because of suspicions that it had brought illegal weapons meant for the Katipunan rebels, but this happened in the context of a very recent Triple Intervention that had intimidated the empire quite a bit, so if you want a more long-lasting and stable Japanese Phillipines, waiting a bit is probably a good idea; the very begining of the Spanish-American war comes to mind. If Japan attacks Spain with a semi-valid pretext (maybe there was SOME sort of gradual scalation of the 1896 incident) before the US opens the Pacific theatre they leave very little room for American complains: the prospect of a cheaper war will trump other concerns in the eyes of the pro war faction. HOWEVER, a big issue here is that the American Pacific navy was stationed at Singapoore, and they moved really fast, so we probably want Japan to already had decided to attack the islands before Spanish-American conflict became aparent, ideally already having a battleplan sorted out. A factor to consider is that because Japan is much poorer, they are WAY less likelly to pay full indemnization for the Spanish infrastructure in the islands (like the Americans did), so it will look like much more of a dick move to the international community and it will give France, who doesnt want anyone with a big navy near its colonies, Russia, who is already in conflict with Japan, and Germany, who
really wants the Philipines for herself, the perfect excuse to throw a fit. Britain however, will provably be willing take anyone but Germany there, so I'd expect a lot of support there. In the end, they'll be able to keep them, but something has to be done about the infrastructure indemnities.
Now there is the matter of
what exactly it is they do once it's theirs. As it was said already in the first page, Japan will very likely take the puppet protectorate way, as this aproach comes with plenty of benefits: 1) It makes ruling it a whole lot easier, and the population will be a lot more agreeable. 2)The prospect of a land invasion of tropical islands against a largely non hostile territory only to be able excert complete control (that they don't even have the means to put and keep in place) and where you are largely dependant on the rebel leader's cooperation to show some form of legitimacy is just... dumb. 3)If Korea has taught Japan anything, it's that any dependent enough protectorates can be annexed later, once complete political control is in place. 4)Now, on the matter of the treatment of the locals, I believe that the Japanese would be pretty lenient with them, while pressing Japanese education. Everytime this has been discussed there is always the tendency to think that a Japanese Philipines would be a ruthless tyrany because of how it was with the Koreans and Taiwanese, who where "even more culturally similar" or something along those lines (IOTL they were forced to adopt Japanese customs and take Japanese names), but I think that misses the point: The Japanese were tyrannical with them because they could afford to be. If they can have a peaceful protectorate by treating the natives as equals, they will.
Finally there are possible butterflies. As long as no naval disasters occur, it doesnt seem to me like the war with Russia can be avoided in the long term. The empire can not allow for complete russian domination of Manchuria if Korea is to be secured, though Russia might be less inclined to underestimate Japan's capabilities.