Ford installed two tire diameters, the 15" tires are about 29" tall, and the 16" tires are about 30" tall. There were a few slightly different tires used, so the tire variance alone would make at least 1/2" height variance.
My 98 Mountaineer I believe is typical of all of these 2nd gen. SUV's. It had a difference of almost one inch from the front fenders to the ground. The fender which was higher had a shorter distance from the ground up to the frame, at the control arm bushing, than the other side.
When I went for my first lowering alignment, I had set the frame to ground dimensions the same. My left adjusting bolt was backed out only a few turns lower than stock, while my right adjusting screw was almost out. My right adjustment would not give the same adjustment as the left side.
When I wore out my first set of tires after 30,000 miles, I reset the heights again. Using a 30.5" tire, new "B" bars, a flipped right adjustment lever, I ended up with a more level front end. The fenders are still not at equal heights, but they and the frame heights are closer than they were to level.
Your goal should be to find a height which won't wear out CV joints quickly, if you have 4WD, and look and ride good. Measure the frame heights, the fender heights, and play with the adjusters until you are satisfied.
Search and read what others have done, listen to what they say about ride quality at certain heights. Adjust your heights to achieve your best compromise between ride and appearance.
Shock absorbers are very critical to ride quality, and going beyond about an inch of lowering in the back will cause bottoming out with loads. I have 1.375" blocks in the rear of my 98, and I am searching for one inch blocks for the rear of my 93/99 Explorer. Good luck.