This is still happening with the latest templates.
I am using instyle (latest template at present) and have just spent ages trying to figure out how to use the logo position to drop a module in under the logo.
I've just discovered this post, which basically says you can't do it (unless you're a PHP programmer with lots of time).
If you have a demo that states 'module positions' , then they really should be available when you go to position a module.
With instyle it appears there is a whole header section you cannot add anything too, you can't use/edit the content in:
- Logo
- User area (which had a message in it 'Welcome visitor you can log in or create an account' which every website has to have (or learn PHP)
- Main menu
Not so good.