Would it not be possible to install a flow rate monitor between the engine and the day tank? If so it would be possible to estimate with okay precision flue usage for any given time period.
I Apologize for the naive question, because I imagine there's a reason it isn't done already.
I've only been on one ship built in the last decade that had that, and you could read the number on a computer screen. (FYI, the computer systems and automation on ships are a joke, if you can do it better than the current companies, you could make some money. Also, tangentially related to why we'll never have fully-automated ships. Stuff breaks, and ships lose money every day they're in port for repairs.)
However not all fuel that goes to the engine ends up being burned. Fuel is always being pumped through the fuel line at a high pressure, and only a fraction of that is burned when the cam system actuates the injectors to inject fuel into the engine cylinders. The rest of the fuel is returned to the tank.
As for the ship I was on that had a more accurate measurement, I don't know exactly what was measured. I can only speculate it was the fuel in minus the fuel out.