Hi Dan,
Yes the initial pages created in a new site are determined by config files in the webroot/Setup/initialcontent/pages folder
You can define pages and put any feature on a page. If you put an HtmlContent module on a page you can also specify a file that contains its initial content but there is not currently a way to do this for other features. For example you can creae a page with a Forum module on it but there is no way to autmatically configure the forum and put initial posts in it at this time.
This same mechanism is used for initial site creation during setup but is also used when you create a new site from Administration > Site Settings
Hope it helps,
Joe