1. Adding the font family option takes up quite a bit of resources due to the amount of fonts that need to be loaded each time. I figured not a lot of people need a completely different font in the footer than the rest of the site, so I excluded it there. If enough people want it I’ll definitely consider it, but I want to keep the Customizer as fast as possible, so reducing the amount of massive font lists is pretty important.
2. The Customizer definitely needs some organizing, I have a really good organizer writing me up a list of what should go where from a users perspective 🙂