The SU10 Navdata API is the name of a set of functions calls that has been added to the the Simconnect SDK which can be used to obtain information about airports and has been added with SU10, hence the name.
It doesn't have anything to do with which kind of "Navdata" you have installed in the sim ( default or 3rd party ). In fact, the whole point of it is, regardless where the data is coming from, be it default or 3rd party and even in case it's encrypted for the Marketplace, addons using the Navdata API like GSX, should always get the right data from the sim.
Or, more precisely, whatever data the sim is using, it will be communicated to GSX which uses this API. Whether that data is correct or not, it's another matter entirely. Meaning, if you have a problem or a conflict ( for example, two sceneries of the same airport conflicting with each other ), when using the Navdata API, GSX will read all, including the conflicts...
So, if you have the SU10 Navdata enabled in GSX, which is done exactly as the manual says: enabling its option in the GSX Config Panel, with nothing else to do other than restart Couatl ( is not even required to restart the sim ), whatever you see in GSX should be what you see in the simulator. You can use the World Map to confirm that.
Note that, any change to the actual installed sceneries ( like changing GSX Jetway replacement exclusions ) or installing/removing/disabling/enabling a scenery DOES require an MSFS restart instead.