This has to exist first...
Thats the new Kickstart.php file.
Then small mod here...
// copy the standard index page
exec("cp /usr/local/ispconfig/server/conf-custom/index/standard_index.html ".escapeshellcmd($data["new"]["document_root"])."/web/index.php");
I just changed the index.html to index.php at the end there...
And now all the new sites are created with a custom index.php file.