The way I see it, is the AIB want us to know that both engines and drivetrain were serviceable and stopped and that the 95 litres of fuel drained was all that remained in the aircraft. Otherwise why bother telling us anything?
The fuel on board at start of ops is known.
The total time of flight is known.
The fuel burn can be calculated.
So with that in mind I am willing to bet that 95 litres is what remained. The supply tanks hold 115 litres, so if both transfer pumps were on and working correctly, then the main tank would be empty and the supply tanks less than full.
Add unusable fuel into the mix and maybe you can see why I think the fuel system design is questionable.