Oh right, i guess didn't make that clear. I was thinking about one portal.
The system redirects to the default portal's first alias if an alias cannot be found.
For the Skin thing, the modules will all be added to the ContentPane if the pane that they are originally assigned to cannot be found, so they will show up anyway.
One way to hide them though is to place a little inline CSS in your Pane elements:
<td id="ContentPane" runat="server" style="display:none" >