@transmitthis - no, I don't believe so. Covers for books are always saved in jpg format, which means no transparency capability. The "brown book" you refer to is a bit of a "kludge" if you like in Calibre, where a book does not have a cover. In that situation the calibre code displays the brown book .png file instead, which does have transparency.
So what I do is use a black background, which gives a nice effect on the cover browser. I don't mind the background being black on the book details panel.
In answer to your question on short stories, what I do is have a bunch of images which represent different genres, and have those embedded in the cover. So there is not a "short story" image as such, just a genre one. The reality has been for the books I have that in 99% of cases if it isn't a short story then there is an official cover for the book.
In terms of the choice of images, what I did was usually find some classic old magazine covers from google images, where the name of the magazine reflects the genre.