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The most suitable tool for comparing Microsoft security baselines to current device configurations is Microsoft Intune. This tool is designed for managing mobile devices and applications and includes functionalities to apply security baselines, assess compliance, and enforce security configurations on devices across an organization.

Microsoft Intune allows organizations to configure security baselines derived from best practices and compare them against the actual settings on devices. This ensures that devices adhere to the established security policies, helping to identify any discrepancies between the desired security posture and the current state.

While Windows Autopilot is a tool used primarily for provisioning devices, it does not have the capability to assess or compare existing security configurations. Microsoft Endpoint Manager is a broader management platform that includes both Intune and Configuration Manager and emphasizes device lifecycle management but does not directly provide the comparison functionality specified in the context of security baselines. Azure Active Directory focuses mainly on identity and access management rather than specific security configuration comparisons.

Thus, amongst the provided options, Microsoft Intune is specifically tailored to assess and ensure that devices meet the necessary security compliance requirements.