I agree with most of your points here. The thing to understand is that these are all tradeoffs. For example, it's true that collapsing flagged subthreads by default is unfair to the users who post substantive comments in that subtree and haven't broken the site guidelines. (Sometimes we rectify this by manually snipping them, so they can go back to the top level, if we see them and they make just as much sense at the top level.) However, it's still a major improvement to thread quality overall to collapse flagged subthreads by default. Moderation is fraught with these tradeoffs, and when we find any major improvement to overall quality, we pretty much have to do it. In this sense we're basically all victims of statistics here.

Re https://news.ycombinator.com/item?id=34838236: that got hit by a simple spam filter. Clearly it was a false positive (another tradeoff—no spam filters without false positives). Sorry! I've restored it now*. The funny thing is, I was just looking at that particular filter this afternoon and realized it might need some work—I just haven't had time to review it yet, which involves looking at everything it has killed recently and evaluating whether it's still doing more good than harm.

* ("Robot war dogs" is linkbait though, so I've taken that bit out of the title, as the site guidelines ask - https://news.ycombinator.com/newsguidelines.html)