Does Zen Cart have to run my entire site?

Is there any update on this request? I've searched around and all threads seem to dead end in the same spot.

I have my webpage with a custom CSM run at http root /var/www/mysite
Zen Cart is a subdirectory of root, /var/www/mysite/store

If I put this at the top of my index in root the session/cookie is created but the zenid is different and knowledge of the actual customer is unknown except for host and ip:
chdir('store');
require_once "includes/application_top.php";

Why is it not finding the same zenid from the session created while in a page under /store/ and is there a solution?

I have custom functionality and custom site CMS for an informative site, so I cannot incorporate this into the EZPages. The reason for accessing the session is simply to show login/logout/myaccount and the cart/checkout options appropriately.