I don't think you are missing anything, Don. Book has some good aspects, and some which are remarkably fiddly.
I am not sure what you mean by "Favorites" - exactly which feature is that? - but in general the font seems to stick to the last one you applied. I'd recommend you save fonts as "presets" in the Type panel, as these presets can then be included in an Auto Layout panel preset. This is a great way to set up your own default style and to start new books with a usable initial layout, instead of dragging pictures one by one. I start all books this way.
But it can still be awkward if you experiment with another font and I'm never totally confident that all my text is my favourite Gill Sans. So at some point when I'm reviewing the book I usually select all the text boxes and make sure they are my preferred font. Selecting text boxes is damn fiddly, and even worse when you want to select all the text throughout the book. My trick is switch to Book's grid view and then use Ctrl Alt A (Edit > Select All Text Cells), then review the Type panel. A bit after the event, but still handy to pick up before they go to Blurb.
Hope this helps
John