IMO the issue is less severe as you say. You should expect in a site of any size to have multiple users that want to use the same username. The user just sees a message that he cannot use his preferred username because it already exists. Only the admin would know that that user does not exist in his portal, and he might "bug" the hosting provider about that. Presumably the hosting provider told the admin that is site is part of a multiportal environment, and as a result, usernames might be registered at different portals.....

If you want them to all be a different universe you'll have to setup multiple databases and instances of DNN. With DNN you can setup multiple portals that share logins, so a user could login to all your portals with the same user information, though this does require a few changes in the data to accomodate.