Philippine Airlines: Victim of a Phoney War?

Probably because the Philippines does not want to be seen to be escalating the tension between it and China. However the aircraft you've identified is owned and operated by China Airlines, a Taiwanese company and not to be confused with Air China, the PRC operator that's partly owned by Cathay Pacific.

Air China and two other PRC operators: China Southern (based at Canton) and China Eastern (based at Shanghai) do fly in Philippine airspace on their routes to Australasia.