If it is record mended or preferred that books use one font for the whole thing, then why do some self-published books have two fonts?

Sometimes for clarity, most of the times because they're self-published and people do whatever they want, regardless of recommendations and what sells. Just look at all the un-proofread self-published novels with atrocious home-made covers that are out there.

I'll tell you what's "record mended", and that's actually reading through your post before hitting 'Submit'.

I can think of commercial books that have multiple fonts. Kate Atkinson's Behind the Scenes at the Museum has sections of flashbacks that are in a different font. It is more of a design issue - too many fonts tends to make a publication look like a ransom note.

I guess each book is different. You can use one font if it is fiction, if it is free verse you can write your book like an artwork