Hi Jamie,
It may typically happen that the home page has pageid = 1, but it is not what makes it the home page and the home page can have any id, in fact in a multi site installation child sites will never have a pageid = 1 since that is typically already used by the first site.
What makes a page the home page is merely the root level page (ie it has no parent page) and it has the lowest sort order. Any page could be moved into the home page position.
I think what he is really asking is when a new site is created how does it create the home page and where does the content come from. The answer is that initial pages are created based on config files under /Setup/initialcontent, so anyone could package mojoPortal such that it has different initial content when a site is created. You can define any number of pages and you can configure them to have feature instances on them. For the Html feature you can even configure the initial content of the html, but other features can currently not be pre-configured other than putting them on the page.
http://www.mojoportal.com/configuring-initial-content.aspx
For example I use this on demo.mojoportal.com to create a set of pages when the demo site is re-created, but the default package only has 1 page pre-configured and that is the home page.
Best,
Joe