This would require adding additional known panels, there is no way to do it with css. Content is loaded/rendered into the panels using server side code based on the panel id and they must be both known and unique.
The problem I see with making a header or footer content section is that it makes no sense to put any feature except maybe the Html Content feature there. It certainly makes no sense to put a blog in the header or footer for example and making it easy to do that seems like inviting problems and support issues. I've been planning at some point to implement and ad rotator system which could optionally be used in the header or footer but in general I think the idea of a header and footer is to be consitent across pages so typically you just put whatever markup you want there directly in the layout.master file.
Still, you've got me thinking and I have an idea for a solution that I will look into that would allow 2 optional content sections which could be placed whereever you like in the layout. The trick is to make it work so that if they are not present in the skin no error occurs and the content just gets loaded in center but if present they would show up as options for contewnt layout. Again these would have to have known server side ids so I would probably name them divAlt1 and divAlt2
When I get a chance to try my idea I'll post again.