I'm afraid we're not aware of a good solution to this.
One peculiarity of Google Classroom is that comments you add to a Google Doc or Slides template are not replicated when you create a unique copy of the document for each student.
And if you share a document with comment view enabled, so that all students can see the comments, then any student can resolve the comment.
Here's an article from Google's help site confirming the lack of a solution:
If you're aware of a solution to this problem, please feel free to add to the comments below!