Good post, something I always wonder about when starting a project like this.
One thing I'd like to add is compatibility. If you need to change this site later to a new design or theme, ideally you'd have those "sections/content" available.
With that in mind my approach would be to either set the sections up as pages or a custom post - but it depends on what the content is.
Some other problems I come against is linking the sections and url routing (especially if you want to link to lightboxed content)