The Spaniards colonized us for 333 years and still retain some of our indigenous cultures and in that time period, we have lots of revolts to the point we can kick them completely if we had external support or were united. Being more brutal than the Spanish might bring a rise in nationalism across the colony.
Differentiated between Spaniards and Japanese is Distant.
Spain where in the Other side of the World when they colonized Philippines.
Japan Close enough to the Philippines that they would have Far more Influential and Controls than Spain or even with OTL US.
You are right about Filipino will fight for Independence for Country, but you have realize something they are not fighting with Spanish or American anymore.
They are Fighting with Japanese who will Fights like Hell, Never surrendered to anyone and Warrior Culture that drilled to Japanese Soldiers.
Yes they will More of Nationalism across the colony agonist Japanese, but There will still be places like Manila will be Heavily populated by Japanese setters across the Luzon.
If Philippines does get Independent, the relationship with Japan will make US and Confederacy into child play.
Aka Philippines will be like TNO mixed of Omsk and NPA type of Nationalism
P.S it is not a Attack of your People and Cultural in anyway. You people are Badass and will the Japanese cause to make their Chechen, Vietnam and Ukraine war with the Filipino who are now have experience to fight to Japanese for 80s years .
No disrespect, just speculating here