Where did you see the referenced quote "Note: Configuration Sync cannot be performed with a combined network." ? I've searched but can't find it, in fact the documentation site doesn't really have any reference to config sync, only working with Templates, and cloning existing networks.
Sometimes it is convenient or necessary to copy configurations from one network to another. If an Organization has multiple networks, it is possible to copy an existing MX or MR network configuration to another network. For MXs in particular, the traffic shaping and content/security filtering settings can be copied.