The Page Order helper within Site Manage allows you to add ANY tool to a site, including those designed only for My Workspace. It seems to bypass the configuration.
For example I can add the Account, Profile and user Preferences tool to a normal project site. In addition the list doesn't show the normal site tools that I am allowed to add (like Forums for example)
IMO the ability to add pages via Page Order is redundant as you can do the same using Site Info > Edit Tools.