Host headers are only needed if you have mutliple IIS sites running on the same ip address so it can resolve which IIS site should handle the request. mojoportal doesn't really care about the IIS host headers other than that is needed to resolve which IIS site handles the request so if it doesn't map to th eone where mojoportal is installed ten mojoportal will not be handling the request. But a mojoPortal installation is only one IIS site even if it hosts multiple sites, so we have to be clear about what we mean by sites, it is a different context to talk about IIS sites vs mojoPortal sites that run in the same IIS site/installation of mojoportal.
The difference between host name based sites and folder based sites is how mojoPortal determines the siteid, for host name based sites it determines the site id based on the host name and for folder based sites it determines the site id based on the first folder segment in the url. So mojoportal cares about the host name mapping in Site Settings that tells it which site is mapped to the given host name, if no site is specifically set for a host name then the root site (ie the first site created during setup) is used. Similarly for folder name based sites, if that is enabled then in Site Settings you will not see host name mappings but instead folder mappings.
By determining the site id it knows which site content to show.
Hope that helps,
Joe