The rubber should crush down to the point where it is not a factor when you tighten the nuts down.
This is very important!!!You must make sure that the center thru bolt of the spring locks into the hole in the upper spring perch when you cinch the nuts down or it wil move on you. Most of the bolt heads are smaller than the hole so there is a built in spacer ring in the spring pads that make up the difference. The bottom plate on the spring is there to take up some of the thickness you lose when you go from 5 leafs to 4.