html snippet references to scripts and css files does not reference CIVICRM_UF_BASEURL

The html snippet scripts and css references fail when collecting email sign ups from a non CiviCRM web site, The reason is that all the url references are indirect.
Here is an example script reference that will not work on another web site:
<script type="text/javascript" src="/sites/all/modules/civicrm/bower_components/jquery/dist/jquery.min.js?r=zRY9k">
</script>

Here is an example css reference that will not work on another web site:
<link href="/sites/all/modules/civicrm/css/navigation.css?r=zRY9k" rel="stylesheet" type="text/css"/>

We have noticed this problem before, but we've been doing manual editing of the html snippet, however this is difficult for even power users to do and the snippet does not behave as the help text indicates it should.

Here's the dialog about this issue from stack exchange
http://civicrm.stackexchange.com/questions/540/why-does-the-html-snippet-for-a-profile-not-include-the-url-of-the-site-for-link

I replicated this on http://d46.demo.civicrm.org

PS there is an empty script reference towards the bottom of the snippet

<script type="text/javascript">
</script>