The B747 300 has 5 main tanks and four reserve tanks. Unless all indicators are working accurately it is impossible to tell exactly where all the fuel is late in the flight.
By the end of the flight the system is configured tank to engine but even then the fuel in the outboard reserves is not drained into the outboard main tanks until 20 mins before TOD, again reducing the chance of the FE spotting a problem.
It is therefore not unusual to end up with a low tank quantity after a long flight but normally the FE has a fair idea which tank indicator(s) are slightly out and pads the fuel in those tanks. If the operator, as reported changed the requirement to stick check the tanks, then it seems to me that the change removed a chance to identify an inaccurate indicator which would have allowed the FE to pad the final balance prior to landing.
I must admit I was surprised that no water drain appears to have been carried out. I often used the presence of water in a sample as a way to identify a suspect indication.But again there appears to be a recent change in procedure from my experience when fuel was water drained prior to each T/O even if fuel was not uplifted
Basically the old system worked on the Classic and the changes seem to be only put in place to standardise the procedures with other types in the fleet.
Having identified a problem ie no fuel in a tank/engine combination that the crew had no earlier warning and an airport right in front of them,I see it as perfectly reasonable to land on 3 engines. Pilots who fly with only 2 engines don't seem to realise how well the 747 manages on 3.
If they had been further out I'm sure they would have manifolded the engine and restarted it and monitored the quantities and fuel flows.
And yes with the exception of transferring fuel from reserves into mains, the Classic B747 has no way of transferring fuel between tanks in flight. On the ground it can be done on the mains by using the fuel dump system.
Overall I can't see that the crew did anything wrong. They just followed procedures and checklists as written and got the aircraft on the ground safely as they were paid to do.
Wunwing