I agree with you, to be called out when seen if applicable, although maybe it would be useful to be able to separate which comments are about such thing than not.
Fortunately, if there is such a top-level comment, any other comments can be replies to that and so you do not need to fill up the top-level comments with such kind of complaints, I think.
If it were reliably contained to one thread I don't think there would even need to be a rule, yeah. I often see it where a bunch of top-level comments are spelling out the same 2 or 3 issues (some in a mean-spirited way), and though I care deeply about software accessibility, that is itself a usability issue for HN.
Fortunately, if there is such a top-level comment, any other comments can be replies to that and so you do not need to fill up the top-level comments with such kind of complaints, I think.