Please do not overthink it. Header Builder is meant to create a custom Header. Footer Builder is meant to create a custom Footer. And Content Builder is meant to build your page content.
You do not want to create a different header/footer for each of your pages, right? Because this is what will happen if you use the header/footer builder for building the entire page.
And Content Builder has elements that are not in the Header/Footer builder.
Hope this shed some lights,