I want to show the apparel subcategory icons 6 across and everything else 3.
So your customizer option should be 3 and this should be your code:
add_filter( 'option_generate_woocommerce_settings', 'tu_custom_wc_columns' );
function tu_custom_wc_columns( $options ) {
if ( is_product_category( 'apparel' ) ) {
$options['columns'] = 6;
}
return $options;
}