Two things run in parallel, and the site knows which one to believe.
The MilACARS client on the pilot’s own machine reports telemetry every twenty seconds and files the complete flight report at the end. While it is following a flight, IVAO/VATSIM tracking steps aside, so the same sector is never counted twice.
What you get from it
The Live Map shows everything that has been airborne in the last ten minutes. Live 3D is a cockpit view of a flight in progress over real terrain, reached by clicking an aircraft on the map.
The view shows where the aircraft was a few dozen seconds ago, not where it is now. That is deliberate: the movement comes from two positions that were really measured, not from a guess.