It depends on how you modify it, what specifically are you planning on modifying? You don't have to indicate the specific changes you're making just how you're going to implement the modification.
Sidenote: I am evaluating cPanel right now if it meets requirements for us and how flexible it is in customizing it for our customers.
In the first step i want to remove the unpacking of the .tgz (see more below), simply modify the WordpressX.pm file and add my own scripts in the "run_scripts =>" section. Once i know more about the cPanel API the plan is to write our own "cpaddon" that would be an alternative to yours customized for us so we don't run into any conflicts during updates of cPanel.
Using a tar archive is not really a good solution in my opinion so we have a different approach.
I am currently managing all wordpress customers with a wordpress version directly from the wordpress git repository. This is done by putting wordpress into a subdirectory and pulling the config and wp-content up one level into the root. Then you just need to so some config changes and it runs just like any other wordpress.
PHP:
// inside the user home directory public_html
index.php // require( dirname( __FILE__ ) . '/wordpress/wp-blog-header.php' );
wp-config.php //customized WP_SITEURL, WP_CONTENT_DIR, WP_CONTENT_URL
wp-content/ //all content users can edit like theme and plugins is in here.
wordpress/ //this is a simple git clone of the wordpress github. It will also be updated with a few simple git commands
This is the birds eye overview of our custom Wordpress management. We would like to keep that in place as it has proven to be a very secure and easy to maintain setup.