I have plenty of long distance flights arriving in MNL very early morning (both from Nth America and NZ). I actually prefer a 3:30 arrival as it means less traffic to deal with, but saying that later morning arrivals have not presented an issue of late.
I always have accommodation available on arrival (usually a cheap AirBNB), so on arrival I go straight to sleep for a couple of hours (as I do not sleep on planes-). At about noon, I head out and look for food. Then I go to sleep that night at a 10 or so, and I am back into routine.
I tend to not overthink jet lag etc.