The deal is, you have to have some sort of master controller for the network. That guy generates a unique network id and when you use it to add units to the network, it sets them up with that id, so that they will be recognized by other units with the same network id.
You can use any Z-Wave master controller to set up your network. However, only the most recent ones will have support for the various new types of units that are out there, such as locks that require the new security stuff and such. They used to mostly be remote control'ish type devices, but now more are moving towards software master controllers, because Z-Wave has continued to add new unit times and most of us who have been doing it for a while have a drawer full of old master controllers that are useless now. Software ones can easily be updated to support new unit types.
But you can use any functional remote, assuming it's not really old I guess. For instance, I can use my old Intermatic HA07 remote control type controller to add all my units to, and then I can replicate this to the VRCOP just fine, and control them via CQC. However, the HA07 is an older remote and it doesn't understand new stuff like secure locks and some other more recently added stuff. But you can do a network completely without the Leviton stick or Leviton software, if you can find a master controller that will support all the unit types you need.
Leviton offers their own software based master controller, and apparently that will only work with their own USB stick. It does support the latest unit types, being software based. When you use it as a master controller, then the USB stick is typically only there to allow the software a way onto the Z-Wave network. It's not generally used for control of the network, though in theory it could be. For instance, my HA07 remote control type master controller can be used to control the network as well as set it up. But, with the Leviton software you instead replicate the network info to a secondary controller (the VRCOP) and that's what the automation system uses to control the Z-Wave network.
An automation system could choose to provide support for a USB stick both as master controller and as the overall control point if it wanted to. Or it can choose to set up the stick as a secondary controller and require you use some other master controller for network setup. That is basically what is going on with the Leviton setup, except one is a 'plug in wall' type unit instead of a USB stick. Our old 'native' Z-Wave driver used the USB stick as a secondary controller and you had to use some other controller for network setup.
Hopefully that helped, though it may have just confused you even more.
