If you only want to ensure top element/tree of your configuration exists (which is not updated), you may try combination of default-operation(none) and then operation attribute operation:"merge" on part that should be updated https://tools.ietf.org/html/rfc6241#page-37 (I have not tried it, it is just suggestion).
If you need to ensure everything exists, then probably you need to write your own rpc operation.