Simply put: they're trying to discourage people from including custom fonts at all
in their ebooks -- fonts that are meant to be used as the default body text, that is. They're not discouraging anyone from embedding fonts to be used for headers and other special elements/sections within the book.
It's been determined that many readers enjoy being able to choose their preferred font for reading. Embedding a font and constructing the ebook in such a way that the default "body" text uses that font, oftentimes prevents
users from being able to change the default font of the book.
As to whether including a font is wise or not. Who knows? I do
know that I still see a lot of commercial ebooks coming from Amazon with Charis fonts embedded in them. But unless the creators get creative with CSS, some Amazon devices are ignoring the fonts. My Kindle Fire HD won't display embedded fonts that are assigned directly to the <body> element with CSS. *shrugs*
10 Kindle Quality Guidelines
Amazon strongly recommends that you verify your exported content before converting it into a Kindle book because some content creation tools format content differently when exported to HTML.
In addition, Amazon encourages you to review the entire book for:
• missing content;
• wrong content;
• alignment errors;
• forced font throughout the entire book; and
• proper paragraph spacing.
These errors negatively affect readability and may require the Amazon team to suppress the title to protect the reader’s experience.