The custom header and footer are just config vars, so they can be overriden in your theme.php as any other config var. Use $config['custom_header_path'] = 'foo/bar/whatever';
$config['custom_footer_path'] = 'foo/bar/whatever';
although I'm strongly opposed to the idea of a theme designer to abuse that variable: you can easily use a regular include in your custom theme, so why remove the feature for the end user: the custom header and footer includes are meant to enable users to include their custom, dynamic content, not yours.
If you should abuse the custom header and footer variables, your theme will not be listed on our demo, as we use the feature to include the overall site navigation and the theme and language selectors in a different way than usual.
If you need includes in your theme, modify the pageheader and pagefooter functions instead of messing with the variables that is meant to provide fexibility to end users. It's not meant to provide a tool for theme designers, and I simply can not see a legitimate point in abusing the variables.
Don't get me wrong: I understand that you're exited about cpg1.5.x and we welcome your contributions. However, I find it a bit pre-mature to start creating a lot of fresh themes for cpg1.5.x as long as there is no public beta you could build against and as long as the theming section in the docs is still pretty empty (because the theming engine may still be subject of change).
This being said, I suggest developing visually and not in terms of functionality yet.