disable debugging (placeholder) blocks for the selected roles.

This is fixed in the dev version, I assume you are actually using the alpha1.

Also, you can select for the branding region/zone to "force render" on the theme settings, which will also resolve the issue.

However I would even suggest you use the Delta blocks module that comes with the latest Delta release @ https://github.com/ThemeGeeks/Delta as that enables all those elements as Blocks.

To set this up properly: Disable (Toggle off) all core page elements in your theme settings ($messages, $logo, $site_name, etc.) and go to your blocks configuration page or Context and then assign the Delta blocks as you wish.

Yes thats how it is supposed to work. Look: The Logo is being placed with print $logo; in the region--branding.tpl.php. However, if there are no blocks available for a region then the region wont get displayed (naturally.. thats how drupal does it). But since you have the $logo in there and want to "abuse" the region (not for blocks, but for static page elements) you have to check "Force render" in order to render the region (and with it ... the logo) even if there are no blocks in there.

The reason that it always shows in debugging mode is because Debugging mode adds a BLOCK to EVERY region!

I still suggest that you use the "Delta blocks" module. Blocks > Static page elements

@luk911

Yes... it will be the default theme setting in future release(s)

As himerus said we will do that in the future. But its still suggested that you use the Block from delta_blocks.