By a configurable transport agent, an example might be an SMTP agent that reads a list of sender names or domains from some location and takes a particular action on those messages...let me know if you have something drastically different in mind.
It really depends on the scope of the agent- is it a routing agent installed on Hub servers that should act on all internal mail? If so, those configuration details should probably be stored in Active Directory-which is fine for MS built-in agents, but for custom agents, you may have to extend the schema which is not to be done lightly.
If it's an SMTP agent install on Edge, the configuration would be stored in the local registry or file system.
I hope this answer helps- let me know if more is needed.