Zblerg, not sure why this fails (the xmpp-upload part) if all the other stuff work …
Are you interested in the xmpp-upload feature ? Otherwise I guess a “simple” fix/workaround would be to not define / delete the DNS record for xmpp-upload, and yunohost will not attempt to integrate xmpp-upload inside the certificate … (Just be sure to wait ~1hour maybe after deleting the DNS record)