The CLI can run a workflow from a workfow.json (or a job from a job.js)
But when you pull or deploy a Lightning project from the CLI, it comes down in a format which you can’t really use with the CLI.
Really you need to be able to run from a project.yaml and specify which workflow you want to run, and it should work just like workflow.json from there.
(There is a GH issue on kit to track this but adding to canny)