1.1 Yes, the vendor mode is to allow firmware upgrade to the EEPROM using the Blaster Plus utility.
1.2 The Blaster Plus code example using the CyUSB.dll isnt available because the HX3 is a fixed firmware part and hence we cant share the vendor commands needed for programming.
2. Please use the configuration settings to customize HX3 as per your application. You could refer to Page 25 in the datasheet for the different customization options available.