My guess? This is what happens when a tech writer who doesn't fully understand a technology is given information about a subject by an engineer and is asked to translate it into proper English. Even more cryptically, earlier in the document, it said, "Do not include the Charis font; it is replaced with a higher quality font in the Kindle Readers."
I'm guessing that the Kindle publishing process involves a human reviewing the book, and if you use that particular font, they substitute Caecilia or something, but it could just be more of a "We don't like this font, and we think ours are better, so please don't include a font under the flawed assumption that the reader's built-in fonts will all suck."
Either way, it's just a guess.