Martin (1992: 100):
… at clause rank, as noted in Chapter 2, substitution and ellipsis signal interpersonal, and thereby experiential meaning as recoverable …
 This mistakes a non-structural cohesive system, ellipsis–&–substitution, for a structural system of a rank unit.
 This mistakes one type of cohesion, ellipsis–&–substitution, for a sub-type of a distinct type of cohesion, reference. Halliday & Matthiessen (2014: 635):
Reference is a relationship in meaning. When a reference item is used anaphorically, it sets up a semantic relationship with something mentioned in the preceding text; and this enables the reference item to be interpreted, as either identical with the referent or in some way contrasting with it.
Another form of anaphoric cohesion in the text is achieved by ELLIPSIS, where we presuppose something by means of what is left out. Like all cohesive agencies, ellipsis contributes to the semantic structure of the discourse. But unlike reference, which is itself a semantic relation, ellipsis sets up a relationship that is not semantic but lexicogrammatical — a relationship in the wording rather than directly in the meaning. …
Sometimes an explicit indication may be given that something is omitted, by the use of a substitute form;