Hello!
If you have the status "Provisioning succeeded" - it means that Defender was installed on your server. This MDE.Windows extension initiates Defender installation, is responsible for the onboarding process, and checks of health status of Defender. Then you should see the server in https://security.microsoft.com/, if not, then check on the firewall if the server can connect to Microsoft services and check the server's network configuration. Most likely the problem is with the network or with the DNS name (maybe you onboarded this server to Microsoft EDR with another hostname).
There is no need to download and run the onboarding configuration package if the status of MDE.Windows is successful. You are right, the onboarding package in the Microsoft Defender portal simply configures the Defender and binds this device to your tenant.
You can also check the status of Defender from Powershell via commands: Get-MpPreference and Get-MpComputerStatus.
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