I have a similar use case. However, as the container I am getting from the repo can be used the fetch information from many different MQTT brokers, I am using env variables, initiated as the start of the container to configure all brokers (url, user, passed, topic, qos…).
So flows_cred is empty… maybe not applicable to your situation, though.
I'm surprised when you say setting the credential Secret in settings.js doesn't work as we have a very similar setup and it works on our side. When you first setup the Node-RED project, are you using the same credential secret as in your settings.js file ? When using projects the credentialSecret is stored in the .config.projects.json file and should be the same as the one defined in your settings file.