That’s a clunky way of saying “when something is different, make it look different.” The best designers, in my opinion, take this to heart and don’t use too many variants to make those differences as clear as possible.

A LaTeX template I used for pimbook. Contribute to j2kun/book-template development by creating an account on GitHub.

To keep things brief: I recommend putting both your footnotes and your references at the end of the book, but separately.