This post shows the ability to allow SCCM to deploy device configuration settings even though the workload authority has been moved over to Intune. This is particularly useful if you have a requirement which Intune does not have available yet but you still want to manage the rest of the device configuration settings from Intune.
To do this you need to manually add the exception in the SCCM Console. If you navigate to your configuration baseline and go to the properties you will see a tick box for “Always apply this baseline for co-managed clients”. After ticking the box you have successfully added an exception and the baseline will continue to apply even if the workload has been moved to Intune.