always calculated as if it were a full flight
You added this, the manual doesn't say anything about "always calculated as if it were a full flight".
There's an *example* that takes a fully loaded 737 just to show how the calculation is done, but that doesn't automatically mean that any calculation is made based on the full airplane.
My proposal is to take this information from Fsx on information that is modified by the menu Fuel and payload
As I've said, the calculation IS done based on the ACTUAL station load of the airplane at ANY moment the number of passengers needs to be calculated.
And besides, this should have been very easy to verify: try loading any airplane with all the stations empty, you'll see the baggage carts will have only 1 wagon.