If the Germans got the PI in 1898, they would have lost them after WWI like the Pacific Islands. I'm not sure how they would have wound up, given their size and population (some sort of protectorate probably) but IMHO they would not have gone to the Japanese. back to the POD. Assuming that Spain still owns the PI in 1941, and Franco is running Spain, there is no need for Japan to attack the PI. The Spanish will present no risk to Japan in shipping goodies from SEA to the home islands, which was the reason they attacked the PI OTL because the US could interdict supply lines. In fact Japan would be happy to bypass the PI because it allows them more forces for SEA, and if they are going to attack the USA for that as well. There are no key raw materials in the PI they desperately need, and they can buy what they need - if Spain has kept the PI I would bet Japan has a much larger commercial presence there than OTL.
If by 1941 the PI are independent (either from internal revolution or ending of some protectorate) unless they are very closely tied to a military alliance with one of the major powers Japan will be at war with, which is unlikely, then the independent PI represents no military threat. Absent some alliance and major power military basing in the PI the PI has no reason to say boo to the Japanese. Staying a neutral, even "friendly" like allowing flights over their territory, passage through coastal waters, selling things like food and so forth, the PI avoids being invaded.
SEA was invaded by the Japanese because it had resources such as oil, tin, rice, and more that Japan needed to run its economy as well as continue the war in China. In 1941 the PI really have none of these critical items. The PI were taken because they represented a threat to Japanese supply lines when the USA had major bases there. No bases, no threat, no reason to invade.