I think it's clear, and I wouldn't worry about the footnotes taking up too much space. Lots of bibles only use half the page for actual scripture, with the other half reserved for notes.
I'd prefer something with hotlinked footnotes, or definitions, but that would be tons of work, I'm sure.
Right now I'm using the great KJV in the book repository, with books in the TOC and the direct page control hack. It works fine, but I'm not fast enough to keep up on Sunday mornings
