I'm all for supporting Unghosting and Never touching the 60 hive pages  directly, but don't understand how you can do this for a Portal.

How would you go about changing the layout of a SharePoint Portal page  definition without editing the Microsoft direct-mode page itself? I'd love to add a custom folder with just my changes, but how would you get the Portal to use your custom pages as the default?

The main concern I can see with editing the direct-mode page itself is that your changes maybe broken with a future hotfix or service pack. If I am able to create my own custom page layouts, how will the SP/hotfix apply to my pages?