This is indeed the expected behavior. The ha-manager command and the maintenance mode it triggers only apply to resources that are currently managed by the High Availability (HA) stack.
If your VM is not added to the HA resources list, the CRM (Cluster Resource Manager) will not track its state or automatically migrate it when the node enters maintenance. For any VMs or CTs that are not under HA management, you will still need to migrate them to another node manually before the maintenance can proceed fully.