@Matt Dillon , Thanks for posting in Q&A. For your situation, I know you have enrolled device with Autopilot Hybrid Azure AD join and then install Configuration Manager client. Based as I know, it is not a recommend method.
For Autopilot into co-managment, currently, Hybrid Azure AD-joined device is not supported. Here is a link with more details:
https://learn.microsoft.com/en-us/managed-desktop/get-started/autopilot-co-management#before-you-begin
For your situation, if you want some workloads controlled by Configuration Manager but others controlled by Intune, we suggest you only choose co-management method to enroll the device. we can use path1 to configure it.
https://learn.microsoft.com/en-us/mem/configmgr/comanage/quickstart-paths#bkmk_path1
If you want all the workloads controlled by Intune, you can only choose Autopilot Hybrid Azure AD joined method to pre-configure new devices,
Hope it can help.
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