New York's airports count passenger departures and arrivals. Each departure and arrival is further classified as international or domestic. If a CDG to JFK passenger clears immigration, I would expect the international-arrival counter to increment.
If said passenger immediately continues to make a connecting flight to JAX, Question: Is there any reason why the domestic-departure counter would not be incremented?
Update: Passenger counting methods are critical to airport planning, which ensures that service & resource capacity is matched to demand (indicated by counting). The discussion (Q&A) and dissemination of travel metrics serve to improve travel. The passenger is only one stakeholder in the travel process: if you want your systems to work for you then maybe questions from travel providers should be considered.
Any questions or comments, that serve to clarify the question, are appreciated.