This is not really true. It might have been the case in the pre version 4 file format, but now there is an explicit reference field. It does not matter what the content of that field is it will always be replaced by the references. REF** is just used because that was used in older footprints and there was no reason to change it. REF** is also the default set when creating a new footprint via the footprint editor.
REF** actually does nothing in the current file format.
%R is used to convert any user text field (a normal text field) into a copy of the reference.
Similarly, with the value field. The main field is by default filled with the footprint name but you can actually have anything in that field and it will still be replaced by the value set in the schematic.
%V is used to create duplicates of that one, VAL** was used in pre version 4 but no longer does anything special as its role was taken over by the main value field.