I remember being told that the ClearML.conf on the client will not be used in a remote execution like the above so I think this was the problem.

SubstantialElk6 the configuration should be set on the agent's machine (i.e. clearml.conf that is on the machine running the agent)

2. Users have no choice of defining their own repo destination of choice.

In the UI you can specify in the "Execution" tab, Output "destination", a different destination for the models/artifacts. Is this what you are looking for ?