BarneyA, I find it easier to approach The Listener with a set of assumptions that may well be challenged by the individual setter. Others will be able to refine this better than I.
One of those assumptions is that the set of instructions for filling the grid can be set aside once that is complete. What you're told to "after filling the grid" (the wording of this preamble) often involves replacing or moving letters in the grid which, of course, contradicts those initial instructions. It can sometimes call for more outlandish actions.
You are right to read the preamble carefully, particularly any modal verbs. The ambiguity can be part of the fun; the solution almost always clears up any confusion.
More art than science, this.