I usually customise the settings from variables.less and then remove any unneeded CSS (like nav-inverse, or the fixed navbar) from navbar.less. I don’t see any advantage of copying it into app.less.
Essentially app.less contains everything, including Bootstrap, which is imported at the top for lower priority. I tend to have several imports in each app.less that include the CSS/LESS for any non-site specific components. Whereas all the site-specific CSS/LESS is written directly in app.less itself.