Seems unlikely. Using comment count as an indicator of poor quality discussion would treat topics with intense interest and engaging discussion like flame wars.

So, I find this explanation hard to believe, especially given that the mods here are active, and that there are other mechanisms for exposing flame wars (including flagging, down votes, etc).

High-quality posts will usually be upvoted by lurkers, ensuring a favorable upvotes-to-comments ratio. But yes, it's a blunt instrument that sometimes has false positives where the mods intervene to turn off the penalty: https://hn.algolia.com/?dateRange=all&page=0&prefix=true&que...