This an extension to the Domain Access module which is used to create many domains from a single installation.
For what I see as a problem is that the domain module uses the node access api's to determine which nodes are displayed on which site. This will work if you only use Domain access, and no other access module like simple access, tac, or Organic groups.
Node access is more a per user where as domain access is per site. Now because the domain access modules have such a good API, Domain Access Advanced is able to turn off the node access integration in Domain access and re-implement it as a query rewrite (which is how node access actually works) so that content can only be accessed via the domains or affiliates that are specified.
This means that then if there is are node access modules they will then reduce the list more to only allow the user to view the nodes they have access to.