Originally I was going to use Context to set all the section navigation. But this last week worth of doing automagical things with Views and Taxonomy has got me thinking that maybe even the navigation can be set via a View. And the pages that show up as navigation options, that list in the term’s field can also be set by a View.
(Show all nodes with term X as options to pick in the navigation, basically.)
VIEWS ALL THE THINGS.
(And then it’ll be easy for whomever on our team to create all the basic settings for a site section, all in one place.)

So that totally worked, although I’m going to keep the Bean option handy for overrides.
Also, for making sure that it doesn’t show the box if it doesn’t have a navigation: http://drupal.stackexchange.com/questions/107412/hiding-a-view-if-empty-when-contextual-filter-is-already-used