There are box shapes that enclose nothing and there are box shapes that enclose freestanding letters and freestanding puncutation. These situations are not specifically covered in the guidelines, so I'll offer suggestions. Transcriber's notes will be needed to explain to the reader.
See 3.1.1 and 3.1.2. Transcriber's notes should be worded at a level that is appropriate to the grade. The surrounding text and vocabulary is a good indication of that. However, since the print readers can SEE freestanding punctuation, I am not sure that a young braille reader is familiar with the term "freestanding." Therefore, I won't use that term here and instead I'll just describe the way the puncutation is presented in print.
Parentheses is substituted for the box shape indicator and termination sign. See Formats 18.3.4.
TN preceding example sentence:
TNBoxes are shown as parentheses in braille. Punctuation marks that are in a box in print are in parentheses in braille and start with a dot 4.TN
Braille the example without the crossouts and the text above the boxes. Words that start with a boxed letter are UNCONTRACTED. Show that letter unspaced in parentheses with its cap sign if it has one. On the next line, braille the example as it is corrected. Precede that with an embedded TN that says TNCorrected exampleTN
TN preceding sentence #5
TNA box that is blank is a double dash in braille.TN
Follow print spacing for those double dashes.