Current ArcGIS Server KML service offers KMZ file extract option with JSON Geometry clipping functionality. This REST service offers great advantage when user needs to pass geometry from web application to request for KMZ file for clients. However, it does not organize output KML elements into catagories that are defined in web service. Although it respects simbologies, kmz does not have folder structure; therefore, user will need to click thausands times just to hide the category.
Current workaround that ESRI support has suggested was to create group layers with definition queried layers. In order for kmz to be created, user will need to run Map2KML geoprocessing function. Even when the MXD is published, it does not provide Query function to the group level. (it does to layer level, but it is not useful). In order for web application to utilize the export KMZ with clipping would be to publish geoprocessing task using Map2KML through model builder or python. This option has only extent filter, and it does not allow user to specify unique geometry filter.
It would be great enhancement if KML service respect the categorical layer and generate folder structures. This would provide simple, useful KMZ with JSON geometry filtering.