Discourse-doctor calls the rake task (inside the container). There were some changes to the rake task in the past day or so.
I submitted something last summer (?) that added to discourse-setup recommending to run discourse-doctor, they I think was never merged.
It might make sense to have discourse-setup run the rake task after the container gets cranked up. (I now run it routinely after I do an install, though I have to wait for the client to do the dns config before I do.)