You certainly cannot modify or use the handout master.
You MIGHT be able to use the notes pages in some way. If there are no existing notes the students could enter some . If there are maybe drag the notes placeholder off slide and add a shape to take notes. This would need to be on th notes page not the notes master. Just thinking aloud I haven't tested this! Maybe you could enlarge and alter the properties of the Footer placeholder to take notes?
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