One option is to configure ConfD to allow the superset YANG module to be in a single file to be returned from the get-schema call. This will allow the NETCONF client to see the entire YANG module, including the ones supported by both the master and subagents, being supported by ConfD.
What you do is to compile and build your projects using the separate YANG modules for the master and subagents. You then place the superset YANG module in ConfD’s loadpath in order to allow that file to be returned from the get-schema call.
You can refer to How to configure get-schema call for more information on how get-schema works in ConfD.