FTE has the concept of the Command Queue Manager. This node is designated as the one QMgr to which the application should connect when communicating with the FTE agents. If the network has been properly defined, connectivity between all FTE agents and the Command QMgr will be present.
The design is one of the ways in which FTE can enforce security. It is possible on the agent QMgrs for the channel from the command queue manager to be authorized very specifically to a subset of the queues and the messages monitored. The design provides a policy enforcement point. Since the FTE security model is weak to begin with, it is important to try to properly use the security controls that are provided.
This design also means that it is not necessary to manage application service account credentials across all the agent QMgrs.
So, yes, use the Command QMgr for its intended purpose. Have one and only one connection factory and properly design and secure the FTE network using the Command QMgr and its channels as a policy enforcement point.