As an extension maintainer myself I've faced a situation where I'd like that my extension's preference dialog could customize the preferences dialog header_bar just like a core app. I'm the maintainer of Patterned Wallpapers[0], an extension which gets you a new patterned wallpaper every day/week, and I've the following designs for the preferences dialog:

Image: http://i.imgur.com/JPxD3LM.png
An stack switcher (GtkStackSwitcher) which would let users browse different pattern categories.

Image: http://i.imgur.com/cAmr4vX.png
A popover menu which would let users set the update frequency and the category of patterns they want.

Image: http://i.imgur.com/PWbJB2A.png
By clicking in a pattern, the new shown view would present a higher resolution preview and let the user add the pattern as favorite.

In summary, I feel that limiting extension devs to write preference dialogs just within the content_area is/could affect potentially more complex extensions to exist (without a messy preferences dialog).

[0] https://github.com/felipeborges/gnome-shell-extension-patterns
*images http://imgur.com/PWbJB2A,cAmr4vX,JPxD3LM