You can't use relative performance graphs really because it includes games where:
a) there's no benefit in running multi GPU
b) CPU limited games
c) other reasons which I can't be bothered to go through
The result is the graph gets skewed.
The 690 is indeed two full fat (slightly down clocked) GK104 680 GPUs.
When discussing how fast the card is relative to its younger brother it's disingenuous to look at things where the extra grunt makes no difference. You could say that in certain games it's not that much faster than a 680 but that is a fault of the software itself rather than talking about the hardware in isolation.
Besides your obvious points being "obvious", You do have to take a cross the board average to compare cards...I'm still having a problem with 95% better in anything !, you saying BF3 ?