I am not sure this is officially a "bug report" or not, but posting it here for lack of a better place to do it

Vanilla install of 1.5.4 gives me 11 errors and 5 warnings as posted by Melanie Prough in another thread. Validation report is here:

HOWEVER, if I use CSS JS loader on my install, i get a clean validation with no errors.

My problem is that I am worried that the code in includes/templates/template_default/common/html_header.php which is causing all the validation errors - specifically:
Code:
/** CDN for jQuery core **/
?>
  <script>window.jQuery || document.write('<script src="//code.jquery.com/jquery-1.11.1.min.js"><\/script>');</script>
  <script>window.jQuery || document.write('<script src="<?php echo $template->get_template_dir('.js',DIR_WS_TEMPLATE, $current_page_base,'jscript'); ?>/jquery.min.js"><\/script>');</script>
is not being called when using css js loader and that this has something to do with PCI compliance and is necessary code.

If I move the 1.5.4 core includes/templates/template_default/jscript folder into the classic directory, I get one error
as can be seen here

Can you help? I have a new site for a client scheduled today and I do not want to do it in 1.5.4 if there are going to be validation errors, or if my installing the css js loader is going to break PCI compliance if that is what these scripts are being used for.

Thanks to anyone who can help!