Windows Autopilot and Configuration Management Client Installation Methods

Please refer this if it helps: 

Co-management settings: Windows Autopilot with co-management | Microsoft Community Hub 

Another hidden value

If your organization has complex applications, you can also add a property in the above command line "PROVISIONTS." When the device gets to the "Device Setup" phase of the ESP (Enrollment Status Page), the task sequence called from on-premises will run and be tracked as one application. For the sake of clarity, if your task sequence installs 10 applications, the ESP will still track the task sequence as one app, because it is watching the task sequence, not each item in the task sequence.

Still want to use the supported MSI line-of-business (LOB) deployment if you choose to install the Configuration Manager agent using MSI LOB deployment? Here's what to keep in mind.

If you choose configuration A shown above, the expectation should be:

• Intune is the authority.
• All workloads are managed by Intune.
• Authority value will be 1.

If you choose configuration B shown above, the expectation should be:

• Configuration Manager will be the management authority.
• Workload management will come from Configuration Manager.
• Make the Configuration Manager agent installation "required" as part of the ESP profile.

Remember, the key defaults to the value of 1. Your authority is still going to be Microsoft Intune, and you will not experience the previous flip-flop issue. If you want the authority to be Configuration Manager, so you can choose which individual workloads come from Configuration Manager or Microsoft Intune, make sure the "Advanced" slider is set to "No." That will make the value become 2 and configuration manager sliders come into effect at that point.