To clarify I meant the software on the Phantom itself, the aircraft, not the app. I do not know for sure, but I think we could agree it is either tracked by the battery or by the aircraft. The reason I think that it is tracked by the aircraft instead of the battery is because of the data present in the .dat file (the file that is only saved on the aircraft that records about 600 points per second). Things that are tracked are all the voltages, the current, the average current, the max current, the remaining capacity in milliamp-hours, the battery temperature, etc... If I were DJI I would want to limit the number of sensors in the overall battery/aircraft system (lower cost, lower weight). So, I would not have redundant current sensors which leads me to think the current sensor(s) is on the aircraft and not the battery, it would save a lot of cost that way. If you look at how the battery connects you could block the gold contacts on the bottom so only the 2 main contracts plug in, this would probably answer the question although I expect you would get a battery error...
Either way, tracking the remaining capacity is most accurate from full charge down rather than from a dead battery up while charging....so....I will continue my practice and I expect my battery will last longer than someone that takes it below say 10%....we can compare our results to see which works better. I consider my batteries to be fairly new, they both still show 100% life with about 20 charges on each....