Strange thing in our environment - we didn't have this policy created at all. We deploy the agent in Autopilot as a required app during ESP. Every single device bar one has ended up with the correct co-management settings (we have some set to pilot Intune, but by and large all clients are set to CM).
We use mostly PXE and USB for imaging still, but autopilot is used in a few scenarios now, depending upon location and local suppliers. And 99% of our estate is W10 - however we have a few pilot W11. One of those was autopiloted in December, and that is the device where the registry key you alluded to is set to 1. We noticed it because the user received a Wifi profile that is only assigned to a few AAD joined only devices that we have. I have checked on another autopiloted device, and since we didn't have a policy set, there was no key (as I expected).
Now I have created a policy, targeting only Autopiloted devices (existing and future) and set the value to 2.
However I'm still confused as to why one device out of 50 or 60 that have been autopiloted so far should end up with the wrong setting. Or indeed any setting at all...