Using a third-party CMS while writing your own HTML/CSS?

I am looking for a free/open-source Content Management System that could be used without using their own theme, or can modify the basic page layout of the website. I looked into WordPress, Drupal, Wolf CMS as well as GetSimple, but they all seem to provide a set of pre-defined themes and will not allow me to build a website from scratch. Would you have some CMS that can allow me to write my own HTML/CSS from scratch and just provide the functionalities of a CMS, or that they allow me to edit the layout/markup of the theme directly in the source code? Thank you in advance! :)