To override plugin’s variable.php with your theme’s variable.php.copy/paste variable.php file from plugins woocommerce/single-product/add-to-cart to somewhere in your theme and then you will need some code in your theme’s functions.php file that replaces theme’s variable.php file as default variable template. Here is such sample code. Replace the/path/of/your/plugin/variable.php with the path of your theme’s variable.php.

function use_theme_variable_template($template, $template_name, $template_path) {
    if ($template_name == 'variable.php') {
        $template = 'the/path/of/your/plugin/variable.php';
    }
    return $template;
}

add_filter('woocommerce_locate_template', 'use_theme_variable_template', 20, 3);