Unlike some other SE sites, I've noticed (and sometimes contributed to) a good deal of discussion in the comments here at skeptics. Sometimes these back-and-forth comments are about problems with an answer, clarifying question or suggestions for improvement, which seems to be appropriate for a comment, as per the description of the comment privilege. Sometimes they involve clarification of a downvote reason, which also seems to be appropriate, though not explicitly addressed in the description of the privilege. Often, though, they don't seem to fit any of these categories.
Since I'm trying to become a good Skeptics.SE contributor, what is the best course of action, here? In my answer to this question, the OP uses comments to try to discuss an element of the original question that was edited out in order to keep it on-topic for skeptics. The original question included references to a non-notable claim about the political ramifications of a drug that was also used for abortions having another use, and mentioned that the author of some of those studies was someone who accused a US Supreme Court nominee of sexual assault. These two facts don't have much to do with the notable claim, that the drug is an effective treatment for a specific condition, but they might make it seem more topical and interesting to users scanning question titles. You can see the history of the question and the response to it in the comments to the OP and the question's revision history.
My instinct is to respond to the comments. In the comments to my answer, I've tried to be clear that I don't think they are on topic, but that doesn't seem to be working. I'm reluctant to flag a comment for not fitting the guidelines for commenting, since they're not harassment, unkind, or obsolete, but I also don't like the idea of letting the comments suggest that there is something missing in the answer, or that the author's speculation is a significant issue. I ended up responding to the issue itself (though I probably shouldn't have) when it was raised in comments on this answer.
What's the best course of action here? Leave it alone? Flag it? Keep responding that it doesn't relate to the question (despite being the OPs question)? Am I misunderstanding the role of comments on skeptics.SE? I can see how it might be important to give the author of a question a little more leeway in comments on answers to his/her question, since the are, after all, the one who asked it. At the same time, if that part of the question doesn't meet the criteria for a question here, the comments could be seen as a way to get around those criteria.