Yep, from the factory, with equal size tires all around, the only E bodies that sat taller in the back were the AAR/TA twins. Everything else sat with the rocker panel level to the ground, which tends to make the body line on the trunk slope down and make it look like the rear is lower than our collective memory recalls. I suspect that is because so many tires were replaced right away with something wider and taller that created the rake that was so common in our minds.
A common practice to raise ride height with leaves is to add a stiffer, over-arced spring to put more camber into the spring pack. Additional leaves also increase the spring rate. I suspect this combo is what the OPs previous owner did to both lift the rear and prevent it from bottoming on dips or with passengers.
Replacing the stock shackle with the three hole aftermarket shackle won't work with E bodies because of the rear valance. The longer shackles will not fit under the panel without cutting it for clearance. It also isn't the most stable method of lifting the body height as the extra length can get side loaded more easily and distort bushings or even bend. Will it happen as soon as you pull out of the driveway, no, and probably not with a lot of easy miles on it either, but they will slowly distort the bushings and with the splayed mounting of an E body, slowly push them outwards at an odd angle.