Windows Server 2016 automatically restart

If you set three policies in GPO like below:

1- No auto-restart with logged on users for scheduled automatic updates installations.
2- Re-prompt for restart with scheduled installations.
3- Configure automatic updating: 3 – Auto download and notify for install.

So,

the no auto-restart with logged on users for scheduled automatic updates installations policy behaviour changed in Windows 10/Windows Server 2016.

Policy no auto-restart with logged on users for scheduled automatic updates installations only applies when Configure Automatic Updates is set to option 4-Auto download and schedule the install.

At the same time, option 4-Auto download and schedule the install only valid if values exist for ScheduledInstallDay and ScheduledInstallTime.

So, although you have configured to not re-start when there are log on users, automatically re-start will still happens at scheduled time.

Below are relate articles, just for you to have an further understanding.

https://docs.microsoft.com/en-us/windows/deployment/update/waas-restart

https://msdn.microsoft.com/en-us/library/dd939844(v=ws.10).aspx

Pejvak you can choose option 2 for Configure automatic updating According to this link to solve the problem too.