Sync’d directories should means that you can save drafts to file in Drafts’ iCloud area, and have those automatically picked up and available in a local repository in Working Copy.
The use of Shortcuts isn’t taking advantage of this powerful feature, but it is enabling automatic, periodic export; so there is potentially a use there which does not overlap with the sync’d directories. i.e. It would be a way of working around automated saving given that Drafts is not editing files in directories.
I think that the two can be set-up to complement each other nicely if both are beneficial to someone.
One suggestion i might make is that rather than adding a path line into a draft, you could store it as custom metadata to keep the draft content clean.