If it shows text then it should work as this text is the extra condition to show only products with avail > 0.
You can change the same code in product.php as well
if (!empty($active_modules['Recommended_Products']))
include $xcart_dir . '/recommends.php';
to
if (!empty($active_modules['Recommended_Products'])) {
$only_instock = true;
include $xcart_dir . '/recommends.php';
}
but keep in mind that this just will hide out of stock products from the tab as well so it won't make much sense to have this extra option.
More coding will be required to separate them like this but I don't see how is ok to show out of stock products on the tab but not ok on the popup?