All style guides (CMoS, APA, etc.) say to put short story titles in quotes. The name of a short story collection would go in italics because it's categorized as a book. As a rule, the titles of books, long poems, plays, and movies (among other things) are written in italics. You use quotes for the titles of essays, articles, short stories, and book chapters (among other things). So it doesn't matter if a story is part of a larger collection or if it's published on its own; the title always goes in quotes. Ha. I'm not any of those. I'm doing law. Thanks for the vote of confidence, though. I'm not sure there's a logic behind it. It's merely convention. The titles of shorter pieces tend to be written in quotes, and the titles of longer works go in italics. Because Dick and Jane is a book, it's considered a longer piece, and the title would go in italics. Even the titles of children's books go in italics because any book is considered a full-length work. You are sort of right about the overarching title thing. If T. S. Eliot's The Waste Land was published on its own as an individual book, you would refer to it using italics. However, if the poem is included in, say, The Collected Works of T. S. Eliot, you would refer to the title using quotes ("The Waste Land").
See, when I read through CMoS, I read the section that included short stories, but it seemed unclear as to whether those stories were collected stories, or individual stories. What I'm thinking about here, say, is a story that is written and then published online. It's never been collected into a book and stands all on it's own. From what I was reading in CMoS, it seemed as though it was assumed that short stories were always part of larger collections. That very well may have been an assumption on my part, but that's how I read it. And with the poems you mention, that is exactly the logic I was applying to short stories, but if you've never seen a short story italicized in actual published works that refer to them, then convention extends to that I guess. I wonder how long it'll be before that changes.
CMoS is just CMoS. It's important to see how short stories are actually referred to. If you read books about writing, or literary magazines, you'll see people discussing short stories, and they always put the titles in quotes. I can't remember ever seeing a short story title in italics, no matter what any style guide says.
The reason you don't see stories in italics is because people follow style guides. I don't think people just arbitrarily decided to use quotes when referring to short stories.
Actually, I was interested in this issue from this discussion and went and did a little research looking at academic writings concerning short stories, and found that, lo and behold, they're all in quotes. So yeah, that's a lesson learned. Interesting because it still makes no sense whatsoever! I still think it should be in italics, but by academic standards/styleguide standards, it just ain't that way! Learn something new everyday.