Just checked the matrix website and flights from Tokyo via ICN and then direct to CEB VIA MNL are $542 on KAL and $563 on Asiana.

Both airlines offer flights between ICN and both NRT and HND, which may be an advantage.

Layover times in ICN can be from 2 to ten hours so you need to check exact times.

If you haven't already done so it is well worth checking the matrix website where you can refine everything exactly as you want.

For the small price difference ($624 vs $542) it may be worth it from both time and convenience to go direct on PAL NRT-MNL-CEB.

It's been decades since I've been in MNL so I have no idea regarding how easy international<>domestic connections are there now.

See: matrix.itasoftware.com