Yes, I have multiple docs in a Book. When I go to package this Book, it does NOT grab all the fonts since some of them are also embedded. I need to package this entire project for archiving purposes. Since font versions come and go, I always archive every part of the project for future revisions.
Give it a try. Create two different docs that have multiple similar fonts and the second one has one extra display font. Place them both in a book. Make a PDF of the second one and place this PDF in the first one. When you go to package the entire book, the display font from the second file will only show up as embedded and will NOT get packaged. Clearly, this font is also being used in File #2.
While this might not be a problem for some, this can cause great problems when I assume that all the fonts were packaged. Some of my projects can have upwards of 50-100 different fonts — a bit much to check one by one.