The other thing to consider is that the persistent navigation should recede into the background - drop shadows on everything would detract from the app's conten

The other thing to consider is that the persistent navigation should recede into the background - drop shadows on everything would detract from the app's content. I would assume that the affordances are also less necessary because the persistent navigation is more commonly used. Anyway, this might not be the reasoning by the designer, and it might not actually work in practice, but it could be one justification... rules are there to be broken.