Customize the output of wp_get_shortlink on your site to replace all shortlinks with standard permalinks.

functions.php

function tweakjp_cust_shortlink() {
    global $post;
 
    if ( !$post )
        return;
 
    return get_permalink($post->ID);
}
add_filter( 'get_shortlink', 'tweakjp_cust_shortlink' );