Jon,
Thanks for confirming my thoughts regarding Element.MdlElementRef and Element.ModelReference.MdlModelRefP.
That was only the first part of my questions however, both of these functions return ints and ElementRef/DgnModelRef are structs. There is no immediately apparent way to me to create these structs from the int values and it is the structs that I need for other native MDL functions.
Any ideas on how to do this?