[Plugin: W3 Total Cache] Trick to minifying .js.php and .css.php files?

One plugin that I am using has a .js.php and a .css.php file that it uses to retrieve options from the WordPress database and uses those variables from wp_options in the CSS and Javascript file.

Is there a way to minify these files using W3 Total Cache? If I specify the filepath to the files, W3TC just copies the files and retains the <?php ?> code and doesn’t retrieve the variables when caching the file, so it doesn’t work properly.