I've seen a few examples:
- A comment on a post about licensing on Software Engineering indicating that the post needs clarification. The post is clear enough to know that it is off-topic. Editing for clarity wouldn't achieve anything. At best, the question may be made suitable for migration, but the best thing would be to go to the Open Source or Law Stack Exchanges and, if necessary, get help on their Meta site to write a good question that fits their subject matter and expertise.
- A comment about editing a post to be more about a specific problem. The question was already about a particular issue, but it is a problem involving coding and the use of coding tools, which is off-topic. There is no way to salvage it for Software Engineering.
- A comment about editing a post to be more specific and provide additional details. When I leave manual comments about this, I'll ask specific questions that would need their answers worked into the question to help properly scope a question or give the necessary details. A vague comment like the auto-generated one is more noisy than helpful to the answer. I believe that a simple close vote with no comment would be better.
Overall, the comments are falling into two general categories: those that provide the wrong guidance to a user (e.g., edit a question that is not likely to be editable into a good question for the site) or unspecific advice (e.g., add details without any indication of what those details can be).
I'm not on the receiving end of these comments, but it feels like they can be discouraging when you're told to edit your question and then it gets deleted by the community or told to edit your question with no indication of what edits it needs to be good.
On top of being noisy and potentially discouraging, moderators cannot remove them when they are wrong. I don't think that a moderator deleting the comment will stop the user from receiving a notification, but it would keep the comments section clean.
Reducing the barrier to commenting on a post is fantastic, but the comments should be helpful.