How to add new args data in $wp_customize->add_setting?

This might be what you are looking for

$args = array(
    'default'    => '#e9ecef',
    'capability' => 'edit_theme_options',
);

if ( something() ) {
    $args['output'] = array(
        array(
            'element'  => 'body',
            'property' => 'background-color',
        ),
    );
}

$wp_customize->add_setting( 'modular_header_main_border_bottom_color', $args );

We are first creating an array for arguments. Later we are pushing a key value to that array with some conditions.