Oh, that was me. As such, let me take the opportunity to explain why these posts were not deleted.
In this case.
- The question was closed when I got around to it
- It was likely to be roomba-ed.
- The comments seem mostly harmless.
- I didn't really see any specific point in deleting stuff that would be deleted eventually anyway and were harmless. The flags did seem somewhat redundant in this view of things, and some of those comments felt mildly enlightening.
As far as I know, there's been no change in the general policy in comment flag moderation. We read through them, and decide as needed.
I admit, I had to think a bit before trying to address the new part of this question. I suppose its useful to start with what SE thinks moderation should be. Every new moderator is told to read a blog post called "A Theory of Moderation". I believe the relevant part of it is here
Even with active community self-regulation, moderators occasionally need to intervene. Moderators are human exception handlers, there to deal with those (hopefully rare) exceptional conditions that should not normally happen, but when they do, they can bring your entire community to a screaming halt — if you don’t have human exception handling in place.
With comment flags - its actually a bit of a issue that's a work in progress, and Shog9 has referred to them as stupid in the past.
On one hand we tell users comments are transient, and that any useful information is in a post proper. On the other hand, losing potentially useful information is terrible. In this case - the comments could be useful in fixing the question or it could go away. Deleting it wouldn't reduce the noise level.
It comes back to human exception handlers. You've raised an exception. We're trusted by the community to handle them. Its not always that clear cut, and there's actually a fair bit of thought that goes into them.
We have a certain amount of discretionary powers - we can accept your flag, or dismiss it and that's it (In theory, we can ignore it too) simply because its essential for the process of moderation. Anarchy is the lack of law. When you have laws that are too strict, and too rigid, you end up with harsh draconian rules instead. That feels off to me, especially with how moderation's worked decently here so far.
I'm not sure what I can say that'll make things better. You've mentioned "unwritten rules". We make the effort to help explain things when we can (and I've spent more time on this than actual flag handling or stuff that gets me reputation). Where possible, we're building that 'written rules' into the fabric of this site and no one gets punished for stuff that's not documented anywhere.
At this point, it feels like a lot of effort for not much benefit, but there you go. This is probably the best I can do at explaining the wider, and seemingly "anarchic" way we do things. Considering flags are meant for someone to take a look at something for most part, at least in my opinion, clearly those flags worked well enough.