Here is a userscript (a simplified version of this one here) which you can run on the site list to see which sites have altered the Help Center homepage:

// ==UserScript==
// @name        Help Center analyzer
// @author      Glorfindel
// @version     0.1
// @match       https://stackexchange.com/sites
// @connect     stackexchange.com
// @connect     *.stackexchange.com
// @connect     *.stackoverflow.com
// @connect     *.superuser.com
// @connect     *.serverfault.com
// @connect     *.askubuntu.com
// @connect     *.mathoverflow.net
// @connect     stackapps.com
// @grant       GM_xmlhttpRequest
// @grant       GM.xmlHttpRequest
// ==/UserScript==

/* global $ */

(function() {
  'use strict';

  var sites = [];
  $("div.lv-item > a").each(function() {
    sites.push($(this).attr("href"));
  });

  var message = "";
  function process() {
    let URL = sites.pop();
    if (typeof URL == 'undefined') {
      console.log(message);
      return;
    }

    let helpURL = URL + "/help";
    GM_xmlhttpRequest({
      method: 'GET',
      url: helpURL,
      onload: function(data) {
        $(data.responseText).find("div.wiki-ph-content").each(function() {
          if ($(this).text() != '') {
            message += "\n" + helpURL;
          }
        });
        process();
      }
    });
  };
  process();
})();

The script's output will appear in the browser console and is just a list of URLs. I just did some simple post-processing in a text editor to make it fit the table in the other answer.

Sites with a custom Help Center homepage