Can you get the themes options page to turn on/off which custom post types are registered?

If you can get a dynamic variable value of the brand, then you can load wanted CPT.

Inside function.php
Create a link to your new function “remove_cpt_multisite”.
Ex:

// Remove menu items for users 
include (TEMPLATEPATH . '/assets/functions/remove_cpt_multisite.php');

The template itself (remove_cpt_multisite.php) :

<?
       add_action( 'admin_init', 'my_remove_menu_pages' );
       function my_remove_menu_pages() {
          $my_brand_variable = "get your variable";
          // According to the value add wanted CPT with a switch
          switch ($my_brand_variable) {
             case "brand1":
                include (TEMPLATEPATH . '/assets/functions/register_cpt_1.php');
                include (TEMPLATEPATH . '/assets/functions/register_cpt_5.php');
             break;
             case "brand2":
                include (TEMPLATEPATH . '/assets/functions/register_cpt_1.php');
                include (TEMPLATEPATH . '/assets/functions/register_cpt_2.php');
             break;
          }
      }
?>