I think Tinstaafl has it exactly right. That makes sense with what I have seen.
There are flow meters both in the main and in the return line, and the fuel flow indicator simply uses the difference between the two.
That's amazing... are you 100% sure? What is the indicator? Is it just the G1000?
The reason I am amazed is because the return fuel flow is going to be very sporadic, with a lot of stop/start in it. It isn't going to drive the standard turbine transducer (most systems use the Floscan 201/201B) very well.