For Restart - you should see in the vServer log that all connections were dropped, vServer restarts every "internal" services and states. But it would not affect pref.panel, since there is no new log file, there is still the same vServer process ID and so on. In other words it restarts internally.
For Server.Shutdown - vServer process must be finished. But, look at
/Library/LaunchDaemons/com.paradigmasoft.vserver_x64.plist
...
<key>KeepAlive</key>
<true/>
It means new instance of vServer will be started if the vServer's process gone. You can not stop vServer without unloading this plist
Something like
launchctl bootout system /Library/LaunchDaemons/com.paradigmasoft.vserver_x64.plist
But you should see at least increased logs' count after Server.Shutdown