I think it's the first one as well. But I also agree that there's a lot of ambiguity, and we aren't taught a lot (as moderators or users) about comment flagging.
I would consider these comments not constructive:
This answer is the best.
Please don't answer questions that don't show initiative.
You obviously have no idea what you're talking about. Please stop posting here.
Internet Explorer is useless. Don't bother supporting it. [as seen sort of in your linked post]
I would consider these comments too chatty:
You give great answers.
Have a nice day!
I've had very similar experiences in the past! Can anyone help me?
I guess the ultimate difference here is content. Many "too chatty" comments don't add anything. They're straight noise, without any benefit to anyone. On the other hand "non-constructive" comments do add something, it's just not something that should necessarily be added.
But I would be lying to say I didn't have a fair bit of difficulty with where to place a few of those, it's definitely not obvious, and these might be ambiguous as well.
We've heard it a million times, but comments should be used to request clarification from the author, or add very specific details to an answer. If a comment doesn't do those things (or any that someone marginally used to the system would recognize as appropriate) but does hold some sort of content, there's a reasonable chance that it's not constructive.
I also tend to use "not constructive" in cases where a comment is mean-hearted, but does not necessarily warrant the opprobrium of a "rude or offensive" flag. That speaks something to the "destructive" idea you put forth, and I do think that that's part of it. Of course, also as we all know, flags should not be used to enforce technical accuracy. So make sure, if you're going the "destructive" route, that it isn't "destructive because it says something that's wrong."
But at the end of the day, I guess an important thing to remember is that moderators are humans who sift through flags. Obviously we should all do the best to choose the right flag in any situation, but I think these two are ambiguous enough that in cases of uncertainty, a mod will read your flag and understand the meaning between the two, especially since the resultant actions are the same for either.