Re separated comment box: When the comment box is not sufficient, I usually put something like "see details in returned assignment" in the comment box. I don't really try to repeat everything I put into the marked up document. Sometimes I add information like "assignment turned in late" or "assignment accepted late due to excused absence." In those cases, the comments are about administrative issues rather than grading feedback. I let the returned document provide instructional feedback.
It seems to work for us!
I would say that Mary's suggestion about the type of assignment is the most practical for your situation.
Uploading of files as an assignment
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