The CSS and JavaScript on the front end of your site is provided by your theme and possibly by your plugins.
Your theme's PHP template files which are used by WordPress to generate the HTML for your pages are tightly linked to your CSS files because, for example, they will dictate the classes that are added to the HTML elements that your stylesheets use to determine your site layout and style the contents. Some of those classes are added by your theme, some directly by WordPress, but in any case it is not very meaningful to say you would start a project with no CSS or JS.
It sounds as if your developer may not be familiar with WordPress. Unless they are going to code the entire theme (including the PHP templates) from scratch, then they will need to use a theme as a starting point and build upon the existing stylesheets.
First, a disclaimer of sorts: It is advisable to build on top of the existing stylesheets and scripts rather than removing them and starting from scratch, and we won't be able to provide support for the custom work your developer does if they have problems.
If you are using Layouts it is a requirement that you use a 12-column grid system (as in the included Bootstrap, for example).
Adding or removing styles and scripts is via the standard WordPress methods.
You should not make changes directly to Toolset Starter theme files, but to the child theme instead which is available from the same downloads page. See the WordPress codex for more information: https://codex.wordpress.org/Child_Themes
I would only recommend that your developer embark on this if they are familiar with WordPress development, as this is custom work which we can't provide support for.