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We try to make our SiteBuilder as user-friendly as possible, and accessible as possible, and currently the way we do that involves our users adding pages with titles, which get automatically translated into URLs.
This automatic translation means that we don't really create a complex directory structure, although this could be a feature in future releases. For now, we just create pages in the way which is simplest and most understandable for most of our users. This shouldn't negatively impact your site in any way, since there is no SEO or navigational downside, and I hope it is sufficient for you until such a time as we can consider adding a subfolder feature.
Nathan: I'm not really sure where you're getting your information from, but I feel that I should correct it, as it is not accurate. There is no such long URL: we use virtual hosts to serve everybody's sites, and each virutal host does have a root folder, which its files are served from.