@yeooandyni, Thanks for posting in Q&A. From your description, I know you are migrating from SCCM to Intune. For the co-managed devices, you can switch the workloads to Intune and uninstall the configuration manager client. Here is a link with the detailed steps for your reference:
For the new Microsoft Entra Hybrid join devices, there's no need to install the configuration manager client on them. We can enroll these devices directly via GPO enrollment. As a note, ensure all the login users have both Microsoft Entra Premium and Microsoft Intune license assigned.
Based on my experience, for the GPO enrollment policy setting, it will create schedule task to run the enrollment command. For the already enrolled device, it will be failed to do the enrollment. You can also consider create an OU to these devices to exclude the GPO. Or create an OU for these new devices and only apply the policy for these devices.
Hope the above information can help.
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