The rudeness is in how she completely ignores the explanation I just gave in the parent comment, of why wide feet would lead to people being prejudiced against you, which obviates her question.

There's no explicit question in the comment of NL's I think you're thinking of, so I imagine you mean that the statements in her comment could be read as implying an already-answered question, which makes the comment rude. That hardly registers on my rudeness detector; unless it's part of a systematic pattern of behavior, it's innocuous IMO.

Still, let me pretend I'm SilasBarta and suppose her comment is rude.

So:

1) I explain why having wide feet leads to people being prejudiced against me.
2) Nancy replies, while ignoring the entire explanation I just gave.
3) [Insert comment I should have made instead of the one I did, which would point out how Nancy just ignored the explanation I gave, but which you don't characterize as obnoxious]

OK, I'm SilasBarta. Nancy's replied to me. Most of my comment seems to have gone right past her and she's replied without having understood me. That means I have failed to make myself as clear to her as I'd like, and I want to fix that. It's her first reply to me, she's not being overtly confrontational, and people often write sloppily when replying to others on the Internet, so let's assume good faith. As such, I reply to emphasize my more detailed explanation of how people with wide feet suffer prejudice, this time without any snitty rhetorical questions (or accusations of bad faith). I might write something like: 'Let me clarify. Although people with wide feet may not suffer much direct prejudice, they nonetheless suffer effective prejudice indirectly because it hurts my ability to signal via e.g. choice of shoes, as I pointed out in my earlier comment.'

The reason I belabor the point is that this issue comes up quite frequently, where people complain that "Yeah, Silas, you had a good point, but goshdarnit, the way you said it gives me sufficient pretense to ignore it wholesale and join the anti-Silas's point bandwagon", and I want someone to finally put their neck out and show me what comment would be an appropriate one to protest the (rude) ignoring of part of my comment when someone replies to it.

I don't believe I did use the way you said what you said as a pretense for ignoring its good points. I do think you might have been right when you tried picking out the pity-oriented subtext of NL's original post, but just because I didn't mention it doesn't mean I ignored it wholesale - it just means I didn't have anything to say in response to it. There are a lot of comments on Less Wrong that make good points - presented abrasively or otherwise - that I don't reply to. (Also, I wouldn't even have complained to you if you hadn't solicited feedback on why people had voted down your original run of comments.)