Thank you, @jcheng! Actually, this is more useful than you might think. I've been wondering until now, "Am I doing this all wrong? Am I violating Joe's Grand Unifying Vision of page layout?" So in a funny way, it's liberating to know I'm not.
Based on your comments here, I reworked a couple of pages, taking more liberties to put stuff where I wanted and how I wanted. The pages work better now.
Thanks, too, for the specific observations regarding layouts and panels. That will guide my design thinking.