By the way, Paul, I've just tried this on my Windows PC. I opened a Calibre folder in TotalCommander, picked up an EPUB file with the mouse and transferred it to the iTunes window, letting it drop there. It safely landed in the "Books" section.
So, I'm not sure our fellow poster's allegation is even true for iTunes. The EPUB file I dragged and dropped had never been "saved to disk" in Calibre. It's just an ordinary, converted EPUB file from a random Calibre folder.