"Oh, I dunno, could be the potentially voided warranty on a $600 item."
FUD. iTunes has a real simple setting called RESTORE.
"Or maybe it's Apple's habit of bricking jailbroken phones with updates?"
Then don't update? The only bricking I've heard about was people updating to 3.1.3 on un-jailbroken iPhones! If you've jailbroken at all you know that every time a new update comes out they tell you not to update until there is another way to JB it.
The amount of FUD in this article and these comments is amazing.