I'm looking for a way to force an empty region to display. I notice Omega does this via a theme-settings checkbox, but I'm unable to track down how it's done.
Regardless of removing the if ($page['regionname']): around print render, the region still does not display unless it's populated with block content. Perhaps injecting content into the $content var somehow?
In a custom theme, the header variables such as logo, sitename and secondary links are placed in a region template called region--branding.tpl.php.. (the variables have to be passed from preprocess_page to preprocess_region so this can work and a template suggestion needs to be made). Once this region is printed in page.tpl.php, it must always be rendered even if there is no block content in that area.