I recently flagged a question as duplicate.
The OP responded in saying they see the overlap, yet still sees the difference in value, following any guidelines I've read on the subject, so a mod should be able to weigh their side.
However, this could take time, and it could be very frustrating to be flagged without a chance to discuss further, even more so without an articulated explanation. The appearance of a flag as a comment furthers the impression of an uncaring flagger.
I've seen many users complain about an unexplained flag.
I would comment back with said explanation, but I lack the privilege to do so. This is in contrast to my own questions and answers, where I can comment.
I believe it should be possible to comment on questions where you have active flags. This would apply for downvotes, except they are permitted later than comments anyway.