Filter super admins from WordPress user list for multisite single site.

filter_super_admins.php

<?php
/**
 * Remove all super admins from a non-main site user list.
 **/
filter_super_admins( $args ) {

  global $wpdb;

  if ( ! is_main_site() ) {
    $user_logins = "'" . implode( "', '", get_super_admins() ) . "'";
    $prefix      = $wpdb->base_prefix;
    $query       = "SELECT ID from `" . $prefix . "users` WHERE user_login IN ( $user_logins )";
    $results     = $wpdb->get_results( $query );

    if ( ! empty( $results ) ) {

      $user_ids = array_map( function ( $user ) {
        return $user->ID;
      }, $results );

      $args['exclude'] = $user_ids;
    }
  }

  return $args;
}
add_filter( 'users_list_table_query_args', 'filter_super_admins' );