It seems it can have different header & footers.
Check bootstrap3 theme.php and voux theme.php
There's some custom header & footer at the bottom of the files...
Just brainstorming as i am not into theming : what happens if you change xml to reflect multiple css files (style/looks) create a layout with setstyle ? Kind of BS3 where there is front site, and admin.. (those do have separate styles).