So the issue is most of the time your device needs to be within a pretty close range of the controller in order to include it to the network. This usually means moving the device close to your controller or moving the controller close to the device.
The USB dongles are nice as they have built in power and are simple to remove from your server, take to the device, run the inclusion (flahsy flashy blue lights) and bring the controler back to your server. Once included, the device can utilize the mesh network for further communication and no longer need to be within range of the controller so long as it is in range of the mesh.
Now one gotcha is the Security Command Class. I believe, at least for the Zwave binding, the controller needs to be plugged into your server and OH running and really close to include the device so you will have to either bring your deadbolts to your server or bring your server to the deadbolts. I’m not sure if the Z-way binding has the same requirements and since you are looking at Razberry or zwave.me you should have a licence to use Z-way.
Finally, you are likely to want to put your controller, no matter what it is, somewhere besides where you put your servers. You will have the best performance if you can put it as close to the middle of your nodes as you can. See Share Z-wave dongle over IP (USB over IP using ser2net / socat ) guide for how you can host your controller on a little Pi Zero or something and put almost anywhere and get access to it over the network from your server. If you are using Z-way, I believe you can do the same but you just have to run the Z-way server software on the remote Pi and use the Zway binding (@mstormi can correct me if I’m mistating how it works).