Symlinks are indeed a mess. It wouldn’t hurt to add an “as is” somewhere in that doc sentence. It says symlinks are never followed but it doesn’t explicitly deny trying to do fancy stuff to adjust symlinks to their new environment or something.
Otherwise I stand by my opinion that if unison works and better fulfills the requirements, you should use unison. (General “You”). Atomic directories sound neat but doesn’t fit super well into how syncthing syncs so I’m skeptical you’ll see an implementation in the foreseeable future.