I totally agree. There's a big reason why "Flat" is in quotes. :)

From my perspective, the idea behind the bookmarklet is more of a way to give people a hint into what their site could look like if they decided to redesign it flat.

Of course there are many functional uses of depth which aren't purely for aesthetics or skeuomorphism. For people who already understand that distinction, it's fair to say this bookmarklet has less value.

But I think there's a pool of people who never considered designing their site flat. This gives them a quick way to see something like that.