Here's why its important to set ride height using something other then the wheel wells:
Above is a front picture of the ROD, arguably one of the better handling 240Zs. Notice how the passenger side front fender and headlight bucket is lower then the driver's side. Although the chassis, frame rails, strut towers, rockers, etc. were straight, the car hit a wall in its previous life on the passenger front corner. The front inner fender sheet metal and upper frame horn from the strut tower to the radiator support was pushed down and wrinkled. It was repaired enough to get the front frame rail correct and the strut tower where is was supposed to be.
Using the wheel well to measure ride height would make the passenger side of the car 1.33" too high and really affect the corner weights and balance. By measuring and adjusting ride height from the rockers the car had cross weights within a few pounds. The passenger front looked a little droopy but the car handled well.