(A knock on the door)
Mr. Ko: Who is it?
(No answers. Mr. Ko opens the door and finds no one at the door, so he closes it. A little later, he hears another knock on the door.)
Mr. Ko: Who is it?
(Again, he opens the door and finds no one out there. A minute later he hears yet another knock.)
Mr. Ko: Who is it, knocking the door again and again?
...........................
Put in an indirect question, the last sentence above will be something like:
I really can't tell who it is, knocking the door again and again.
Rather than considering 'it' part of a cleft sentence structure, I'd see it as a demonstrative pronoun.
However, if you add 'that is,' the sentence will be:
I really can't tell who it is that is knocking the door again and again. (Still makes sense, wordy as it is.)
In this case, the functional status of 'it' becomes ambiguous, at least to me. Would it be part of a cleft sentence going together with its partner 'that', or just a demonstrative pronoun, with 'that' being viewed as a relative pronoun whose referent is 'who'? I am not so sure.