Coming from ModX, I like the idea of having the default "home" page be in the heirarchy with the other pages instead of looking like the parent. I think I will go this route and rename the root parent to "Web" like in ModX (Or maybe "Your Website" or "Root"). I think this method will also make it easier for clients to understand. Also, it makes things a little bit easier when it comes to navigation not having to specifically tailor the navigation to include the root page.
My question is, how do you think this will affect SEO? Is it better just to set the index file to a different name in .htaccess?