I think I've reached my limit with the factual information we have available for now.
As I see it to sum up;
Is the 76 kgs left in the main the big clue?
As I think we have concluded, the transfer pumps must have been on during the flight, 20 kgs seems to be about the most that will syphon (or whatever the effect is) from the main to supply after the pumps have stopped pumping, and with an airspeed below 80kts there are about 76 kgs unusable should the aft fuel pump not be pumping.
It is likely that the non urgent tasks completed on the way back in, and the final part of the flight trace were were done at 80kts or below. Without a better timeline we can only assume that at this stage the gauges were indicating 47/76/43, plenty to have a quick look around the city on the way back to base.
But it's that moment at around 22:00, when the supply tanks were the only source of fuel, that has to be key. Why wasn't it realised that even without the warnings, with 76kgs in the main that the supply tanks were getting pretty low? I know this happens in normal flight to a certain degree, but I've only seen the supply tanks go down as far as about 38, anything below 35 despite the caution, would start to raise a few hairs.
One thing that sticks in mind from the report is "The forward and aft transfer pumps, situated in the main fuel tank, and the prime pumps in the No 1 and No 2 supply tanks were tested and found to operate correctly in accordance with their factory specification."
Would that (bench?) test ascertain that the pumps would also operate correctly in situ?
Here's waiting the next update, with perhaps the GPS trace and twist grip positions mentioned.
All the best