Although I released a Magento module “Root Category as Homepage“, which enables replacing the default CMS page with the root category as homepage, thus the users can start layered navigation from the very top level of category, the usage of this module should be limited, for the sake of usability.
In short, use Magento layered navigation only to narrow down the choice of products. Do not use it for the purpose of grouping products by some filter attributes. There are many other ways to group products together.
I will explain in details when I have some more time.