This is a cool idea. If I read it correctly, are you suggesting that MDN create a parallel doc tree, like "web apps", that introduces HTML/CSS/JS with the specific aim of building vanilla web apps? I am sure that it would be popular.
Yeah! Though a similar tone to framework documentation, so it would have to declare some opinions on things (Templating must use the <template> element and custom elements, data fetching outside of the initial load must use fetch(), etc) and the surrounding glue code you have to use to compose all of these APIs together is described to you. (rather than just describing the APIs, like most of MDN's docs)
I think there's easily enough API surface area to cover every part of a front-end web application without any dependencies.