Firstly I don't work for QF so I am not an apologist for them.
I do have about 15,000 hours as an FE on all models of the B747 Classic so I have some idea of what was going on.
What I don't find in the ATSB report is any comment that the aircraft was under fueled so I think it can be assumed that the fuel was on board, hence my earlier comments that it is difficult at an INSTANTANEOUS point in time to know exactly what quty is in a specific tank. We have to remember that the design of the FQI system goes back to the 1960s and is basically unchanged .
All that has been altered is replacing the old indicators with new ones which are LCDs.
I also suspect that human factors came into it in as much as there was probably a seat change on the panel at about TOD, when the FE returned from rest, so he wouldn't have the advantage of knowing the indication trends.
Finally QF have been a very large operator B747 Classics since 1971. Going back through the ATSB site there appears very few fuel problems over 37 years. So even after the procedure changes, it is hard to say they had a major problem. In this case, the crew appear to be following a fuel leak checklist and shut down an engine and that is the only reason that the ATSB got involved .
Wunwing