Unfortunately, only certain parts of the Django admin site can be overridden on a per-app basis, as it says in the documentation:
Not every template in contrib/admin/templates/admin may be overridden per app or per model. The following can:
- app_index.html
- change_form.html
- change_list.html
- delete_confirmation.html
- object_history.html
Remember that the admin interface is itself and app, so it's going to do a single template sweep and load the first set of templates that comes up.
I think your two best bets are either to use multiple admin sites in your project or to add a custom view for specific apps -- the former is probably easier, but will be a problem if you don't want people to have to login separately to control certain things.