Actually, flying into NRT then onward to MNL on JL isn't always expensive. I've done it a few times, and those times, it priced cheaper than going through HKG. One other option is to fly into PVG, then take PR into MNL. It'll have to be two separate tickets, but then you can maximize flying time on AA metal.

Looking right now, it seems like flying through NRT and then JL to MNL is very expensive, so it's probably a very variable thing.