You are saying that MODx is killing Apache’s mod_userdir module? What I don’t understand is how they could possibly be conflicting, unless you have the user home directories as subdirectories of the directory you’ve installed MODx in? I think you may be confused. Or are you saying you can’t access the site you’ve installed in your user directory by that directive? If the latter, this is possibly because mod_userdir will not report the server name properly for the MODx auto-path detection to find.
Yes, pages outside Modx. In a normal apache with no Modx, an index.html located in a user’s public_html directory can be refered to directly as http://domain.com/~username. After installing Modx this is no longer possible.