Are you able to set wp root per project or change it at all? I’m using https://github.com/roots/bedrock-capistrano and it doesn’t seem that wp-cli.yml does not work for our installs.
You are able to adjust the config for your sites as required and then save it as a template. This will save everything in the conf, app, and logs folder. Considering it saves the configs you can change the root that way. As far as wp-cli.yml goes, you can drop one into the app folder and if you cd into it then it will override the wp-cli.yml in the root of the container.