How to reference a function from a class in a different file which is also namespaced?

Firstly, to do this the register_metaboxes() method needs to be static:

public static function register_metaboxes()
{

}

Then, for the callback you pass an array with the full class name including the namespace:

$args = array(
    'register_meta_box_cb' => [ 'FrameWork\Helper\Metabox', 'register_metaboxes' ],
);

If, for whatever reason, register_metaboxes() isn’t static (i.e. you’re using $this) then passing the class name isn’t enough, you need to pass an instance of the class:

namespace FrameWork\CPT;

class CPT {
    public function register_custom_post_type()
    {
        $meta_box_helper = new FrameWork\Helper\Metabox();

        $args = [
            'register_meta_box_cb' => [ $meta_box_helper, 'register_metaboxes' ],
        ];

        register_post_type( 'plugin-cpt', $args );
    }
}