Fuel drainage
No matter what the final attitude of the aircraft is, not all of the fuel would be able to drain from the supply tanks to the main- and there would always be some significant residual fuel left if the aircraft was at its observed final angle. The overflow holes are at the top of the tank. This is probably one of the reasons the AAIB have stated they are confident that the empty supply tanks and 76kg in the main is the fuel state of the aircraft at the time of the accident.
For tank 2 to be empty (and the corresponding fuel filter to be empty) then this supply tank must have run dry, and this correlates with the XFER pump being off.