I rarely use the Terminal & SSH add-on, so I’ve only just noticed that I appear to have two identical sets of folders on my RPi, one under config and one under homeassistant… Is that normal?
Yes. They are the same physical folder, with links for both names.
HAOS uses Docker containers (eg. each addon like SSH run in their own container). Containers have a file system that either comes from an image that was installed or your existing file system. Changes to files in the image do not survive an image update, so any file that needs to remain must be mapped to your existing file system. The name of the mapping within a container does not need to match that outside the container. Many of the HA addons map /config within their container to the same physical folder. The actual location of /config is:
/mnt/data/supervisor/homeassistant
You would see this by connecting the Pi to a keyboard & display, or if you’ve enabled SSH over port 22222. You cannot see this within the SSH addon because it does not map that folder to the same path, and you can only see what has been mapped.
I use “Advanced SSH & Web Terminal”, which seems a bit different to the one you’re using as I get /config but not /homeassistant. For some reason that addon seems to be mapping the same folder twice within the container.
Wow! Thank you! 
the reason you can use " cd config " in the / folder(of the “native” ssh/terminal ) is because there is a “symlink” ( config → homeassistant )
run cd /
then ls -la , then you see the symlink