That's not possible!
You can clone sites only using differents domains or subdomains.
sudo site example.com -clone-from=sub.example.com
sudo site example.com -clone-from=example.org
Subfolder option is suportted:
sudo site example.com -clone-from=sub.example.com -subfolder=/test
Clone sub.example.com/test to example.com/test
And thanks, I will check the Nginx error you mentioned, it shouldn't happen, Webinoly should be able to detect this case and give a proper error message.