Why does plugin_url append absolute file path?

Firstly. it doesn’t look like you’re using the $src for your wp_enqueue_script
Then from the Codex I found the following similar code:

wp_enqueue_script('my-script', get_stylesheet_directory_uri() . '/js/my-script.js');
wp_localize_script('my-script', 'myScript', array(
    'pluginsUrl' => plugins_url(),
));

Perhaps try the following:

wp_enqueue_script('nova-payflow-plugin', get_stylesheet_directory_uri() . '/js/my-script.js');
wp_localize_script('nova-payflow-plugin', 'pluginValues', array(
    'pluginUrl' => plugins_url(),
));

But change the $src value above which is:

/js/my-script.js