Let's ignore the amount of flags in question - bulk flagging is bothersome and that bother is certainly indicative of how things went by in the other discussion but it's also tangential - the actual reasoning that the mods went with, and that I agreed with, is about the comments themselves.
If you see a comment like that which is completely worthless and doesn't contribute to the post, then that is entirely appropriate to flag. But what makes it not worthless? This isn't always inherent. It depends a lot on what we define as signal.
In this case, I'd like to purport that some requests for clarification are themselves signal. There are questions where if I post an answer, and someone pokes in a comment "Did you talk about X?", the thought behind needing to ask about X is valuable. X may be a critical component of the solution that is useful.
In turn, the author sees that X is missing and so he edits it in, and then says in response "Thanks, I edited X in". Now, that comment doesn't do much on its own. But without that comment, the initial signal is unanswered - no one has a direct answer to whether or not X is spoken of. As such, this meager edit comment actually turns into a kind of co-signal, one that symbiotically exists with the existing comment to say "Hey, X is a thing I should've talked about, so I did!".
But that then says, "should we delete the exchange as a whole afterwards? If the edit's done, the question needn't be asked," I says, this isn't always the case. Sometimes the exchange is still helpful signal to have on the situation. In some cases, it speaks to the importance of X, it almost serves as an extra highlight to the presence of X. In fact, like right here in this very answer, FEichinger asks me about this very passage I am writing now, I think it's actually something really important and should've been included in the first revision, but it passed my mind. I think it's valuable signal to keep that FEichinger had to ask me this. There are incidents on the site that will mirror this, probably with less grand gestures but in the spirit of "X is actually that important to point out" or "X is something to be aware of" and that sort of jazz.
That is a kind of signal we may or may not like. I like it, though. Not every request for clarification is actually useful to keep, but some are. I think the ones that are shouldn't be flagged or otherwise taken care of. But if it's pretty clear that we don't really need it, then we can flag them.