Ah, I was expecting this post-mortem after seeing that second custom flag. I just expected it to be asked on Meta Stack Overflow, rather than here.
As stated already, although perhaps not quite clearly enough, moderators cannot provide an explanation for comment flags. We have only two options: "delete" (which automatically marks the flag as "helpful"), and "dismiss" (which automatically marks the flag as "declined"). So, we can either delete the flagged comment or not delete the flagged comment.
The reason it's set up this way is that none of us is suppose to agonize about comments. Our official guidance on processing comment flags is here; specifically:
Note: don't be too concerned if the occasional comment flag is declined; comment value is often subjective and moderators are encouraged to process flags quickly - in most cases, it's no big deal if comments persist a bit longer than needed.
That pretty much covers everything you need to know. It would be a massive waste of moderator time and resources if we had to write a custom message on every declined comment flag, and it would just lead to all comments being deleted by lazy moderators, which is a cure worse than the disease. The correct course of action is to flag comments you think should be removed, and then go on about your day. If the moderator agrees, and they're removed, then great. If the moderator disagrees, and they're kept, well then who cares? Always better to err on the side of caution, and keep comments that may add value to a post (assuming they're not rude or offensive), and this is precisely what I do.
If you desperately want a response from a moderator, then flag the post to which the comments are attached. We'll then be forced to attach a message with our decline, but it'll probably be snarky. My response certainly would have been; I interpreted your second flag message ("Why did you decline my flag without even leaving a comment? The guy asks a side question, I suggest to him that he should ask a real question, that's a classic "too chatty" flag, no?") as something akin to: WTF idiot? Why aren't you doing your job and deleting what I say obviously needs to be deleted?
For what it's worth, I, like Brad, consider flag decline reasons to serve an important pedagogical role. If one of the "canned" decline reasons doesn't perfectly fit the message I want to convey, I will take the time to type my own. It doesn't take me that long, because I'm a very fast typist; besides, I think it's worth it. We do get a lot of spurious and nonsense flags, like those in Brad's gist, but the only way people are going to learn to stop raising these flags is if we tell them why they are unwelcome. Comment flags don't get the same attention because they just don't matter as much.
Regarding the specific comments that you flagged, I declined both flags for two reasons:
It's completely unreasonable to flag the other party's comments for deletion during an ongoing discussion. In this case, you were actively engaged in the discussion, and had just posted a comment reply of your own. If it's only been a few hours or a few days, and the other user hasn't yet seen your reply, then the initial comment should not be deleted.
That is very unfair to the other user, and it just creates confusion. In fact, I consider this to be an abuse of the comment-flagging privilege, a way to get comments removed simply because you don't like them or disagree with them, not because they are actually causing any problems to the site or violating any of our rules.
The question that was asked in the comment was completely reasonable and obviously applicable to the answer on which it was posted. One of the stated purposes of comments is to seek clarification on posts, and that's precisely what the user who left that comment was doing. It wasn't "too chatty".
Yes, your reply was that you considered it to be unrelated, but I very much disagreed with that. You are, of course, entitled to your opinion, and entitled to refuse to answer it, but since it was an ongoing discussion…see reason #1.
By the time the second, custom flag was raised, the conversation had proceeded further. The user responded, arguing that their question was relevant, and then you gave in and posted an answer. I deleted the intermediate comments, which had now become obsolete, but chose to keep the initial question and your response, because I felt they added value to the answer. Of course, you had flagged the comment containing the initial question, so since I wanted to keep that, I had little choice but to decline the flag.
You had previously flagged other comments on that same answer, and I had deleted those because I agreed they were obsolete or otherwise no longer needed. In the interest of full disclosure and context, this is the answer, including deleted comments:
The top two were the ones I deleted in response to a flag as obsolete. The third is the one you flagged twice, and the ones after that are as described in the text above.