The thing to understand is that relative urls are always relative to the root of the web site, so even though we use relative urls there is a difference between /home.aspx and /mojo/home.aspx even though they are both relative urls.
So if you create the content with site running as a virtual directory in the mojo folder for example, the friendly urls have /mojo/pagename.aspx for the friendly part and /mojo/Default.aspx?pageid=x for the real url. So the cleanup would invlove removing the extra segments from the urls if the site were moved to a root level.
The FCKeditor image browser also uses relative urls as does the link browser which allows browsing and linking to pages within a site, so there may be urls in the content that need fixing as well. Of course the normal link dialog ues fully qualified urls as it can link to external pages, but if you use it to link to local pages those urls may also need fixing.
So, its much better to populate the site using the same url structure that it will have in production use to avoid the need for cleaup as much as possible.
Hope it helps,