Mattg, I travelled southbound a couple of months ago: load factor was just above 80 per cent. A friend travelled MNL - SYD - MNL in November 2015 with the southbound 95 per cent full and the northbound 85 per cent.
In September 2015, the latest available month,
Bureau of Infrastructure, Transport and Regional Economics suggests that load factors were 65 per cent in each direction as you state Mattg. This equals an average of 283 passengers a one way trip: normally there are more travelling southbound. The capacity of a 5J A333 is 436 with its 'high density' (euphemism) configuration.
In the same month QF was at 90 per cent northbound and 97 per cent southbound, so using an average of say 93.5 per cent that equates to 278 passengers per trip based on the Version 2 seating of an A333 (297 seats capacity.)
Even at 65 per cent ocupancy, 5J is on average carrying more passengers than QF if the latter has seat occupancy of 93.5 per cent.
Admittedly 5J's yield per seat may be much lower than QF's but QF has now been forced to discount much of the time to sell seats on the route. 5J said a little while ago that the route was not yet profitable but I suggest that as time goes on and more are aware that it operates a single route to Oz, seat occupancy and revenue will increase.
5J's cost per available seat kilometre must be somewhat lower than PR's and significantly lower than QF's. PR is now operating daily and 5 J and QF five times a week MNL - SYD - MNL so I assume that both made rational decisions to increase seat capacity. (Then again, airlines are not always accused of being rational.)
September is low season for travel to Philippines so in December and January 5J's load factors would be highly likely to rise, although February and some other months may again have lower load factors outside of Easter and school holidays. Time will tell.