Publishing Context Variables

I have set up context variables that should handle the publishing of some of my specific content types to publish them into a different directory than where they are really located. The publisher seems to be following the context variable definition, however it is also publishing the content items as they appear in the folder structure.

Here is an example for erauCenter content type, these content items reside in the directory //sites/worldwide/campuses/central/.

Publish html pages to filesystem(1):

'/campuses/' + $sys.template.prefix + $sys.item.getProperty('rx:sys_title').String + '.html'

Site Folder Assembly for HTML in Pages(301):

'/campuses/' + $sys.template.prefix + $sys.item.getProperty('rx:sys_title').String + '.html'

When I run the publishing for this site I get the items populated in the //sites/worldwide/campuses/ directory like I stated in the context variable but I also get the folders and content items published in their normal directory //sites/worldwide/campuses/central/.

I set up the directories in this manner to restrict access to who can edit these content items, but I don’t want this structure reflected in the url to the page.

Is there a way to have the publisher only publish the items via the context variable specified for the content item?