Does it make since to you?
Absolutely, as I told you above, this has nothing to do with your problem and the settings dont have to match with your system as ISPConfig does not write them in the current versions.
If you want to solve your problem, just create a dns record in the dns manager, there is no relevant setting in the system settings module for this so dont search there for settings.
Also is there a script to restart ispconfig3?
No, as there is no daemon that could be restarted.
You seem to mix up the way ISPConfig 2 and 3 work.
1) There are no global nameservers ettings in ISPConfig 3 similar to the settings in ispconfig 2.
2) There is no own webserver and daemon process in ISPConfig 3, the server configuration is done by a cronjob.