My only thing with flying extreme long haul with PAL is that it's too long in one seat! 15+ hours and then to have to land and stay/transit out of Manila sucks. I'd rather take a flight to anywhere else in Asia for a positioning (Tokyo, KL, Singapore, Seoul, Taipei, etc) with an overnight layover and fly direct into Cebu. The bonus is I always get to explore another city, I can easily adjust to the time change, and I just love Tokyo so I tend do do that route lol.
But if you're planning on going to PG before Dumaguete then it makes sense to go into Manila, I just hate it.