Override plugin with functions.php

You can change the name of add_gpp_gallery function both in the callback and in the declaration to avoid the conflict between the original and your clone.

Something like this…

add_action('wp_head','jason_add_gpp_gallery');
function jason_add_gpp_gallery() {
    if ( is_single() && 'your_post_type' == get_post_type() ) ){
        remove_shortcode('gallery', 'gallery_shortcode');
        add_shortcode('gallery', 'gpp_gallery_shortcode');
    }
}

… should work for you.

Bonus: You can remove the original plugin action with remove_action() if needed.