A host set can be specified in multiple custom configuration channels. However, settings in different custom configuration channels are not merged. The agent settings in the custom configuration channel with the highest priority (the lowest priority number) will be used.
For example, suppose you create multiple custom configuration channels for the same host set, each specifying an entirely different set of non-overlapping (partial) agent configuration settings. Even though the agent settings are not repeated in the configuration channels for the host set, the result will be that the configuration channel with the highest priority number (the lowest priority channel) will be ignored. The agent settings in the channel with the lowest priority number (the highest priority channel) will be used for the hosts in the host set. Any agent settings missing from that channel will use the agent default values described in Agent Configuration File Reference.
You can see custom configuration channel priorities using the GET https://HX_IP_<address>:<port_number>/hx/api/v3/host_policies/channels API endpoint.