I definitely think its is possible that the ppl who're put in to controlling the Philippines know what they're getting themselves into and are rather moderate in what they do (considering that Tomoyoshi is a southerner) means that he could easily leave the Philippines to his christian supporters while having the more traditional samurai get land redistributed from former supporters of Tomoshige or the lands in the north alongside Moritora. It really depends on how the situation is handled.It depends on the temperament of the local shogun that will take over, and whether he'll tolerate the existing institutions and framework that have taken root and even blossomed relative to their OTL counterparts.
On the other hand Philippine Samurai would be so cool, imagine them running around with kris, garabs and igorot head hunting axes.
I defo see the Japanese being able to crush organised resistance with the taking of Manila and not being brutal to the natives for being Christian (considering Tomoyoshi is a Southerner he should be more lenient to Christians anyways) or being dicks to the natives or pissing off the other major players in the region (the Dutch, French and Brits are fine with the Japanese taking the Philippines I think?) so it could be a lot less brutal than the Imijin war.I can't help but have this sinking feeling that the brutality of this war OTL's Imjin War, however lucking out with Spain being so weak at this point in time.
Piss-off the occupying Japanese lords and warriors enough and they'll really look down upon the Filipinos the same way the English did towards the Irish. From there - all bets are off since they'll henceforth consider this region as a special basketcase, as opposed to an integral territory. The old, puppetised colonial government? Autonomous and marginalised domains? An increasingly-subjugated food-producing colony like Ireland? Even a Haitian-style plantation? Who knows? It's just that it's very likely that the Japanese will always see the people of the archipelago as something beneath them far into the future.