Halliday And Matthiessen (2014: 686):
With modality, it is very clear that certain grammatical environments constitute metaphorical realisations of modality. … (see Figure 10-3).
Here the cognitive mental clause I don’t believe is a metaphorical realisation of probability: the probability is realised by a mental clause as if it was a figure of sensing. Being metaphorical, the clause serves not only as the projecting part of a clause nexus of projection, but also as a mood Adjunct, just as probably does. The reason for regarding this as a metaphorical variant is that the proposition is not, in fact, ‘I think’; the proposition is ‘it is so’. This is shown clearly by the tag; if we tag the clause I think it’s going to rain we get I think it’s going to rain, isn’t it? not I think it’s going to rain, don’t I?. In other words the clause is a variant of it’s probably going to rain (isn’t it?) and not a first-person equivalent of John thinks it’s going to rain, which does represent the proposition ‘John thinks’ (tag doesn’t he?). …
What’s happened here is that there has been a realignment in the realisational relationship between semantics and grammar. … in examples such as the one analysed in Figure 10-3, a modalised proposition is realised as if it was a sequence, by a clause nexus of projection. The effect is that the modality and the modalised proposition are separated, each being realised by a clause in its own right: the modality is realised by the projecting mental clause and the proposition by the projected idea clause.