A 1" lower ride height does not put the control arms parallel to the ground, they will still slope down from the pivots to the ball joints. Because of how the FSM measures the ride height its easy to know this, the factory spec puts the ball joint 1-7/8" lower than the pivot. So, you have to lower the car ~2" from factory to make the control arms slope the other way.
So yes, you will get better geometry out of the factory suspension than what is published in that article just by lowering the car ~2" from factory. Peter Bergman runs lowered with a 1/2" taller ball joint, I'd be willing to bet those numbers are better again.