On p. 34 of Jan09 commarts, John Berry talks about Doctorow's use of acronyms and letter/number combos as being natural: "They're part of the flow, not an interruption of it." But when typesetting the pages, John doesn't use small caps, so the acronyms stand out and visually interrupt the flow of text. So I wonder if someone could clarify.
I think I made my reasoning pretty clear in the article, though you may disagree with it. Ironically, in the CA article itself, they did use small caps in typesetting my examples. (As I would have myself, in any other context but this.)
I do think the regular capitals stand out, but in your defense I do appreciate the difficulty of setting a text that includes words like TiVo and MySpace, and being prose, perhaps there is more wiggle room, except that you say you still used small caps on the TOC - is it because you wanted it to have more formality?
And back to regular caps standing out, you might even say they are supposed to be that way - they are often brand names and results of marketers who fully intend for them to stand out - a purposeful interruption of the flow.
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