“My first theory was that they had flown the jet to the Philippines, but it seems they didn’t have enough fuel for that so obviously that was out.”
How do you know how much fuel was put on board that aircraft. For all we know the fuelers of the aircraft were Muzzies, were in on this op, and loaded max fuel which means they could fly up to 9,400 nautical miles depending on the 777 model it is.
Besides that, the captain can always call for more fuel load if he feels there is any need for more.
It would be easy to come up with a reason for more.