All of that only adds complexity in the calculation, not the measurement.
The engines have predictable fuel consumption patterns. Even if fuel move across a bunch of tanks, you can still calculate total onboard fuels and detect a leak.
That’s what it already does though. We get a total fuel figure in the flight deck (FOB) and a figure for how much the engines have used (FU - measures flow in the pylons). Add the two together and if the resulting number isn’t what the flight started with then there’s a leak.
The engines have predictable fuel consumption patterns. Even if fuel move across a bunch of tanks, you can still calculate total onboard fuels and detect a leak.