The thread on last week's Listener has almost doubled in length since I last visited. After reading the debate about the role of the symbols in the endgame I don't really see a problem. The unclued letters must be grouped with symbols to provide the cryptic instruction. It can be read as 'In X, Y' rather like a cryptic clue, i.e. in l/c.
For the outline the symbols must surely be ignored for the sake of symmetry. I agree that there is a technical ambiguity, but I took 'them' ("Finally, connect them...") to refer "the unclued letters" in the preceding sentence.