All of the recommended saddle height procedures I've seen are based on the distance from the bottom bracket's center line to the saddle top and thus, independent of crank length. If your "perfect" saddle height needs to be changed to accomodate longer cranks, the cranks are really too long.
What you gain by lowering the saddle is offset by what you lose by having to bend your leg too much at the top of the stroke. Your own posting above made this point.