I purchased yesterday GSX and I first thing I found is that I tried to do a ferry flight in PMDG 737 and asked boarding by mistake and boarding took as long as with passengers even when I set in FMC empty flight.
It's entirely normal, because GSX cannot possibly know anything about the number of passengers, which is a custom setting used by 3rd party airplanes, and it's not supported by the sim itself.
The only thing the sim use, is the load of the stations, which might be a mixture of passengers, cargo, pilots, etc. Unfortunately, the sim doesn't tell us the "type" of a loading station, which is just a name. We can only read the weight and the position.
So, as explained in the manual, assuming the total station load is an unspecified mixture of passengers+cargo, GSX uses the industry standard formula of dividing the total station weight by 220 lbs., which is roughly what a passenger + luggage weights, in order to estimate the number of passengers, which drives the loading times.
So, the only thing that affects boarding/deboarding times, is the total weight of the stations, which is read when you start the service so, you must be sure to change it before calling the affected GSX service.