I’m sure there are regional differences in what we say for different situations, but my use of ‘set up the table’ would be: The table is not in the position it needs to be, or it is a folded table, and it needs to be set up (assembled, unfolded) in a particular place—and possibly a tablecloth placed on it. To set the table, to me, means to put utensils or pencils and paper on it in preparation for a meal or meeting.
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