Portal level  search only returns documents from team  sites where the user  has permissions. In my testing, I have found that even SharePoint administrators do not return portal  search results  if they are not explicitly given permissions  in the team site. However, administrators can go to the team site  and do searches within the team site and return results. I think this is the difference between SQL full text searches and SPS searches.

The reason that Administrators have access  to
documents is the same reason that someone at your company could take
ownership of the data on your C: drive. It would be poor planning to not
loose access to data because an employee left or forgot their
credentials.

General portal  permissions are stored in the Home Area (the top-level
Web for the portal site  Collection). When you create a team  Site from a
portal you are creating a new top-level Web in a _new_ Site Collection.
It does not inherit anything from the portal. The Web Part Gallery, List
Template Gallery, and Web Template Gallery, the Cross-Site Groups, etc.
are all established anew.

Site Groups are anew in every Web and always default to Reader,
Contributor, Web Designer, and Administrator, (plus Content Manager and
Member in an Area). This can only be altered using something like
ExecuteUrl in the Configuration section of the site definition.