The way that zb_cli_init is currently coded, it isn't possible to add any additional USB classes.
zb_cli_init calls app_usb_init, adds the classes it wants and then either calls app_usbd_power_events_enable or app_usbd_enable depending on the configuration.
The documentation for app_usbd_power_events_enable says that all classes should be added prior to calling it. This means that it isn't possible to add additional USB classes (for say a second CDC ACM port or the DFU trigger library) if the zigbee cli is enabled.
Similarly, app_usbd_class_append says that it needs to be called after usbd is initialized and before its enabled.
Currently, I think that the only way to work around this is to make a copy of zigbee_cli.c and use a modified copy rather than the original.