UPDATE: I haven't tested this yet, as I don't have Vista Upgrade media to test, but I'm told that Microsoft's internal documentation does explain how to clean install Vista using an Upgrade version. It appears to be more of a workaround than a true clean install, however. Here's what it says.
1. Boot with the Windows Vista Upgrade DVD.
2. Click "Install Now."
3. Do not enter a Product Key When prompted.
4. When prompted, select the Vista product edition that you do have.
6. Install Vista normally.