@Heimdallr, Thanks for posting in Q&A.
In general, Microsoft Defender for Endpoint is an enterprise endpoint security platform designed to help enterprise networks prevent, detect, investigate, and respond to advanced threats. Here is a link with more details:
Microsoft Intune is a cloud-based endpoint management solution. It manages user access and simplifies app and device management across your many devices, including mobile devices, desktop computers, and virtual endpoints.
https://learn.microsoft.com/en-us/mem/intune/fundamentals/what-is-intune
That is to say, they are different cloud service provided different functions. To integrate Microsoft Defender for Endpoint with Microsoft Intune, it can help you prevent security breaches and limit the impact of breaches within an organization. You can see more benefits with the integration in the following link:
https://learn.microsoft.com/en-us/mem/intune/protect/advanced-threat-protection
The Endpoint security policies are designed to help you focus on the security of your devices and mitigate risk. In fact, the settings found in Endpoint security policies are a subset of the settings that are found in endpoint protection and device restriction profiles in device configuration policy, and which are also managed through various security baselines. If we configure the same setting in different place, it will causes conflict. So to avoid the conflicts, please only choose one place to configure the setting:
https://learn.microsoft.com/en-us/mem/intune/protect/endpoint-security
Hope the information can help.
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