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. One is that there is nothing in the grammar to stratify them with respect to. Unlike NEGOTIATION, IDENTIFICATION, CONJUNCTION and IDEATION they are not a semantic resource with diversified lexicogrammaticalisations — there is no such thing as incongruent (i.e. metaphorical) SUBSTITUTION and ELLIPSIS, nor is there a semantic motif running through the grammar which disperses their realisation.
 This misconstrues stratification. Substitution–&–ellipsis is lexicogrammatical system that realises semantic choices.
 The reason there is no metaphorical substitution–&–ellipsis is that it realises textual meanings, not ideational or interpersonal meanings. There is ideational and interpersonal metaphor, but no textual metaphor. Metaphor itself is a resource of the textual metafunction. Halliday & Matthiessen (1999: 398-9):
One manifestation of the second–order nature of the textual metafunction that is important for our purposes is grammatical metaphor. Grammatical metaphor is a ‘second-order’ use of grammatical resources: one grammatical feature or set of features is used as a metaphor for another feature or set of features; and since features are realised by structures, one grammatical structure comes to stand for another.
Halliday & Matthiessen (1999: 401):
But ideational grammatical metaphors typically have a discourse function of this kind; they are as it were pressed into service by the textual metafunction, to provide alternative groupings of quanta of information.