Custom Drupal admin theme per role
Regarding "Menu > Settings" , You can able to select 


Source for the Main Links (Primary menu)


  Select what should be displayed as the Main links (typically at the
  top of the page).


Secondary links


  Select the source menu for the Secondary links.


For example, If you created a new menu called Header Menu and added some links, now you would like to display Header Menu as Main Menu on top of page which is nothing but Primary Links. In that case you have to set "Source for the main links to " Header Menu.


Reading these values


Yes, You can able to read these values using below code

$primary_menu = variable_get('menu_main_links_source', 'main-menu')
$secondary_menu = variable_get('menu_secondary_links_source', 'user-menu'),



Regarding menus based on roles


You can try using Menu Item Visibility Module


  This module exposes configurable and extendable visibility settings
  for menu links. For example, if you want to create a 'My account' link
  that points to /user, both anonymous and registered users have access
  to the /user path, so both will see the link, even if anonymous users
  do not technically have an account.