Theme Options
For theme options we use Kirki Customizer Framework which is a complete toolkit for WordPress theme developers. Please check out their documentation on how to add panels, sections and controls.
Options Folder
Customizer options are auto-loaded from /models/theme-options/ folder, you don't need to include them. You can delete existing options if not needed or add more as per Kirki Customizer Framework documentation.
Priority
If you open theme-options.php file inside /models/ folder you will notice that there is an array to define priority for customizer panels/sections. Priority can be easily added for new panels/sections.
De::$priority = array(
// ...
);
$priority is a static property of Class Defaults which lives inside Helpers namespace.