Martin (1992: 388):
In spite of the fact that SUBSTITUTION and ELLIPSIS are used to link items cohesively between clause complexes, English Text has not treated them as a discourse semantic system. There are two reasons for this. … The second reason is that SUBSTITUTION and ELLIPSIS presume grammatical functions, not meanings. At clause rank, they have to be defined interpersonally, with respect to Mood and Residue; at group rank specific nominal and verbal group experiential functions are similarly presumed.
To be clear, in SFL theory, substitution–&–ellipsis is a grammatical system that sets up textually cohesive (non-structural) grammatical relations (Halliday & Matthiessen 2004: 561-2). All lexicogrammatical (wording) selections realise semantic (meaning) selections. A comprehensive theory of semantics accounts for the meanings realised in wordings.