In Windows 2016, Server Manager starts up at logon. It does this in Windows 2012 R2, but I have not confirmed whether the solution is the same to prevent this behavior. To stop this, you do from the Task Scheduler.

You bring up Task Scheduler under Administrative Tools.

Expand Task Scheduler Library/Microsoft/Windows, and go down to ServerManager.

Under Server Manager, you will see two tasks: CleanupOldPerfLogs and ServerManager.

Right mouse click ServerManager and select Disable. This will turn this behavior off for all users that login to the server.

I have verified that can be modified the same way in Server 2012 R2 as well.