Colin holds a special place in the cast of The Faerie Queene characters for being the only one to have appeared in another work of poetry by Spenser: The Shepherd's Calendar. Referring to a character from his own poetic canon, Spenser becomes much more self-consciously poetic (as in, obviously thinking about his own poetry through his own poetry) during the pastoral interlude at the end of Book 6.
Colin Clout is a singing shepherd characteristic of the Pastoral genre and is often understood to be a representation of the poet himself within his own poetry. Did we mention Spenser was becoming more self-consciously poetic?
The connection between Colin and Spenser himself is further hinted at when Calidore interrupts the vision of Gloriana and the Graces. Gloriana is the title Spenser uses to refer directly to Queen Elizabeth I in the poem, and so the fact that Colin's music evokes the only, brief image we have of Gloriana in the whole Faerie Queene suggests that Colin holds a special place in Gloriana's esteem, something Spenser would really like to cultivate with Elizabeth.
So, just as Gloriana and the dancing Graces are Colin's vision, Colin making music for Gloriana and the dancing Graces is Spenser's vision. Yeah, being self-consciously poetic gets confusing.