the services queue (where the scaler runs) will be automatically exposed to new EC2 instance?

Yes, using this extra_clearml_conf parameter you can add configuration that will be passed to the clearml.conf of the instances it will spin.
Now an example to the values you want to add :
agent.extra_docker_arguments: ["-e", "ENV=value"]https://github.com/allegroai/clearml-agent/blob/a5a797ec5e5e3e90b115213c0411a516cab60e83/docs/clearml.conf#L149
wdyt?