Of course, I didn't find a similar report until after I had started installing the update.
But let me confirm:
The 2.0.1 update for the iPhone released today does in fact overwrite firmware and undoes what the PwnageTool allowed.
I haven't yet tried to use the 2.0.1 .ipsw with the PwnageTool, but I doubt it will work.
In fact when installing 2.0.1 after the pineapple log popped up it was followed by a cartoon of Steve Jobs with his hands in the air and a 'say' bubble over his head, which I didn't look at fast enough to read. Then it went to an apple logo like the un-jailbroken boot screen.
It seems the update is actually a re-image of the iPhone operating system. I'm going to try using the PwnageTool on the 2.0.1 ipsw and see if that works.
Edit: PwnageTool does not yet work with the 2.0.1 firmware.
Edit #2: PwnageTool Has now been updated to work with the latest firmware.