Yes, installation of the CM Agent is only supported after Autopilot has completed.
Doing it during Autopilot may break Autopilot provisioning.
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I'm using Windows Autopilot to build my machines with AzureAD hybrid join. Currently as part of the ESP we deploy the configuration manager client and our VPN software (both Win32 apps) to them so we can get them co-managed ASAP. We also do this in ESP as blocking apps to control the device availability to users until they are completed. Our implementation partner advised us to install the Configuration Manager client in this manner to speed up co-management.
Autopilot works (albeit slow at _ 60 mins).
I am confused though on whether or not adding the configuration manager client into the autopilot build in this manner is supported? Reading this (Co-manage internet-based devices - Configuration Manager | Microsoft Learn) it states:
You can't deploy the Configuration Manager client while provisioning a new computer in Windows Autopilot user-driven mode for hybrid Azure AD join. This limitation is due to the identity change of the device during the hybrid Azure AD-join process. Deploy the Configuration Manager client after the Autopilot process. For alternative options to install the client, see Client installation methods in Configuration Manager.
So reading this it seems what we are doing is invalid. So question 1:
Furthermore I read here (Co-manage internet-based devices - Configuration Manager | Microsoft Learn) that it appears there is no longer a need to to deploy configuration manager client as an app at all but it can simply be configured in it via Home -> Device -> Enroll Devices -> Windows Enrollment > Co-management Authority
You no longer need to create and assign an Intune app to install the Configuration Manager client. The Intune enrollment policy automatically installs the Configuration Manager client as a first-party app. The device gets the client content from the Configuration Manager cloud management gateway (CMG), so you don't need to provide and manage the client content in Intune.
Is this method only valid post autopilot?
Yes, installation of the CM Agent is only supported after Autopilot has completed.
Doing it during Autopilot may break Autopilot provisioning.