Martin (1992: 388-9):
The difference between presuming grammatical items and presuming meanings is illustrated in [6:4] and [6:5] below. The lengthy monograph in [6:4bi] does not refer to any particular grammatical unit in [6:4a]; it simply presumes meaning that was there implied:
[6:4] a. It took several months of writing b. i. but in the end the lengthy monograph was complete ii ?? but in the end the lengthy one was complete
This has the reference relation the wrong way around. The reference in this instance is cataphoric, not anaphoric: it refers to the lengthy monograph. In SFL theory, the nominal group the lengthy monograph is not a reference item.
To be clear, reference is a semantic relation between elements, whereas substitution–&-ellipsis is a lexicogrammatical relation (Halliday & Matthiessen 2004: 538, 561-2).