@Borut Puhar , From your description, it seems a managed and compliant device can't apply app configuration policy with error "not applicable". If there's any misunderstanding, please let us know.
Firstly, could you let us know the device enrollment type we configured for the app configuration policy? Did we choose Managed device? Selecting Managed apps as the Device Enrollment Type specifically refers to apps configured by Intune configuration policies on a device that is not enrolled in device management, whereas Managed devices applies to apps deployed through the MDM channel and thus are managed by Intune. We can see more details in the following link:
https://video2.skills-academy.com/en-us/mem/intune/apps/app-configuration-policies-overview#apps-that-support-app-configuration
Hope it can help.
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