My perception is that there are more than 5% of cases where the downvotes don't seem to align with comment quality or questionable placement. However, I had never really given this much thought until the last day or so. So, I don't really trust my own perception at this point.
I agree with much of the rest of your post as well, but especially this part caught my eye. How many people even have a proper overall view of what's happening in the comment sections of the articles? I know I don't read even nearly all the articles, so there's a lot of room for perception bias. I imagine it's the same for a lot of people. Additionally, like you said, there's also room for difference in how the quality of comments is evaluated by different people. 'Good' times if you really want to get to the bottom of this!