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The reason why i asked this is because Intune policy description says that it can be applied to windows 10, windows 11, and windows servers but i was not able to find any documentation which indicates that Intune supports server onboarding on MDE.
I'm just another Intune user, so take this with a grain of salt, but while you can manage them in the Intune portal with CM's help https://techcommunity.microsoft.com/t5/core-infrastructure-and-security/how-to-manage-microsoft-defender-on-windows-server-via-intune/ba-p/3713195, as I understand it you would need to install the onboarding package using either a local script, GPO, CM, VDI scripts, or Defender for Cloud https://learn.microsoft.com/en-us/defender-endpoint/configure-server-endpoints