The clean install option via the Upgrade Assistant will keep the same architecture as your existing install, and thus cannot be used to "upgrade" your system from a 32 bit copy of Windows to a 64 bit copy. You have to actually wipe the drive out and set up a fresh copy after backing up any data you want to keep. The Clean Install method using the upgrade assistant will indeed perform an upgrade install (thus the reason you cannot change from 32 to 64 bit... any time you hear or see the word *upgrade*, this is not possible), but will not bother preserving any of your existing files, applications, or settings.
I've amended the FAQ page to (hopefully) make this clearer for everyone.