@OliverS, Thanks for posting in Q&A. In general, when the same setting is configured in both GPO and Intune. The GPO will take effect instead of the configuration in Intune. Then one policy MDMWinsOverGP comes and when it set value as 1, the Intune policy setting will win over GPO and it will take effect. But it only applies to policies in Policy CSP. But for migration, to avoid conflict, the recommended method is to configure it only in Intune and remove the policy in GPO.
For the error when you stop the service, it shows you don't have enough permission to do this. Not relate with any CSP policy configured.
For Microsoft Intune Management Extension', this is a very important component and will be used when deploy PowerShell script, Win32 application and Microsoft Store new app. It will automatically installed during Autopilot phase. When the service is stopped, something like app deployment during Autopilot will be affected. And Autopilot will be failed. Could you let us know why you want to stop this service?
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