(Note: Your thread is in the after 1900s section instead of before 1900s, so I suggest you tell the mods)
Well remember, during the sino Japanese war, japan managed to destroy the Chinese navy and military, but then the triple intervention happened, and japan backed down. If, japan did manage to take the philippines, then the same thing will happen in china where france, germany and russia will intervene and force japan to give up a lot of their claims.
Plus, I don't think 1890-1910 japan has the industrial might to handle a Philippines campaign. I mean, yes 1890s-1910 japan managed to handle against Russia and china but that's because china and Russia(Manchuria) was close to the Japanese islands, so logistical problems are not as problematic. However, unlike china and Manchuria, the Philippines is far away from japan, way far away compared to the failed objectives of the Siberian expedition, and Taiwan. Also seeing how your thread is set in the early 1890s, which means Taiwan has only recently become a colony of japan, that means that the Taiwanese industry, army bases, and naval ports which would be essential for your hypothetical invasion of Philippines would be nonexistent. In addition, this is 1890s japan, way before the rapid militarization of Japanese society, and industry in the early showa era, so japan doesn't even have the industrial, and military might that it had during the 1930s era. In short, I would say that the Philippines campaign would be a lot like the Japanese Philippines campaign in ww2 but a lot worse and one that would fail immediately.