The Mesh protocol that exists for the 9xtend was the first rendition of the Mesh code created almost 7 years ago. At that time, the API interface only offered TX and RX frames.
Now the New XCTU NG software is based off of the 3rd generation of the Digi Mesh protocol found in the XBee products which offers a large API interface. This New API interface which has yet to be added to the 9XTends code offers network mapping, rout discoveries and much more. This is why you get the message you are.