And for the last 2-3: could you write them (I don't have access to them) and present some rationale?
I think it's useful for the the community to see what kinds of comments get flagged, and why. So here goes (these are listed most recent first):
Comment: "@DeboraWeber-Wulff It would be cool to carry a scythe."
Post: Presentation time is out in a scientific conference
Flagged as: too chatty
Comment: "[Best wishes for the overzealous comment deleter.]"
Post: PhD application denial - Is it usual to ask reasons/recommendations?
Flagged as: not constructive
I handled this flag, so I can comment further on the rationale. This post is not an appropriate place for a complaint about comment deletion. It's entirely possible that the "comment deleter" would never even see it, since it's not directed @ anyone. Instead, every future visitor to this post would have to read it... for what purpose? It does not improve the post in any way. If you want to start a constructive conversation about comment deletion, meta is the place to do it.
Comment: "You don't mention a country/system in which you applied. If you applied to a particular professor, you can get some informal feedback; if to a university/department - it's unlikely to get any feedback (see answer)."
Post: PhD application denial - Is it usual to ask reasons/recommendations?
Flagged as: It wasn't flagged. It was deleted after the user added the requested information to the post, presumably making the first part of your comment obsolete.
Comment: "@xLeitix I turned it into an answer, thanks."
Post: Is there a lack of oversight of how professors interact with students?
Flagged as: obsolete.
I handled this flag, too, so I can comment on the rationale. This comment is meant to notify a user of something but has no additional purpose beyond this notification. Generally when handling this kind of flag, , I check to see if the user it's directed @ has been on the site since the comment was posted. If so, I will delete it. Otherwise, I wait a little longer.
Please, if you have to remove my comment, DO inform me.
Since the purpose of removing comments is to remove "noise," it would be counterproductive for moderators to inform you by adding a comment. Also, there is no way in the moderator interface (when dealing with comment flags) to add a comment, so it would involve extra work to go to the post and add a comment.
I think a better way would be for the website to notify you automatically when a comment of yours is removed. If you want, you can suggest this as a feature request on Meta Stack Exchange (if it hasn't been suggested already).