Template hierarchy consist of templates, but not every template file is necessarily in hierarchy.
Essentially hierarchy determines entry points (one of matching templates with pre-defined name structure), but from there template can further load additional arbitrary files.
page-templates directory holds custom templates for pages (is_page() branch in hierarchy). It’s recent development that they can now reside in sub-folder.
content-*.php templates are called by Twenty Twelve like this from other templates: get_template_part( 'content', get_post_format() );. They are named arbitrarily and not part of template hierarchy – just a code organization choice that developers of this specific theme made.
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