so here is my setup. Setting a specific Page to be used on the frontpage via Options -> Reading ->Front Page.
I have created a theme with the index.php for interior page views as well as a home.php for the home view. This is no different than any of the other themes I've setup for client. Per the template heirarchy the home.php template will be used if present and the user is at the site home.
When I surf to the site root I'm served the index.php instead.