There is no reason why this does not work on a linux system or any other properly setup server. The index.php was dropped in favor of spider friendly urls and that such customers wanted. Now if your on a linux server I would suggest you check your htaccess file in your webroot and make sure you have this in there and the page should load fine.
Code:
Content visible to verified customers only.
Now as far as if you want to go back to legacy code sure edit topmenu function and add this in bold where noted approx line 3100 and a little way down you will see the other HOME link as well.
Code:
Content visible to verified customers only.