How to rewrite CPT-Permalinks the correct way (incorporating meta-box-data)?

It’s a bit simpler to let WordPress handle generating the permastruct when you register your post type. I also recommend against using global variables, there are API functions for most of what you need to accomplish with the rewrite class.

function magazine_issues_rewrite() {

    add_rewrite_tag( '%issuenumber%', '([^&]+)' );
    add_rewrite_tag( '%issueyear%', '([^&]+)' );

    // post type registration, other args removed for clarity
    $args = array(
        'rewrite' => array( 'slug' => 'issue/%issueyear%/%issuenumber%' ),
    );
    register_post_type( 'issue', $args );

}
add_action( 'init', 'magazine_issues_rewrite' );

I’m not sure whether or not that will fix your problem, I haven’t tested your full code.