The top of the spring sits on a spring perch that's mounted to a bearing that's bolted (with three small bolts) upside-down inside the fender. The bottom of the spring sits on a perch that's clamped to the top of the damper body. The spring sits between these two perches.
The nut you are wondering about in the original post just keeps the damper rod in place - too loose and it will rattle, too tight and it will damage the threads and maybe the rubber bushing it sits in the middle of. Other than that, it has no effect on the ride height.