T-Case drops are going to be found more commonly on vehicles with a slip yoke and that are not running a CV driveshaft. With the Rubicon one of these would be used if you are running greater than 3.5" lift and no CV driveshaft.
A 1" body lift used in conjunction with a 1" motor mount lift will give additional lift for tires (BL) and reduce driveshaft angles (MML). This will also allow a better TC skid to be installed which will reduce high centering and give better protection!
Another option is adustable upper rear control arms used to match driveline angles to reduce the vibrations. This may not work if the lift is too high, since the driveshaft to yoke angle may still be too large. Then a Tom Woods CV driveshaft with Teraflex shock relocators will be needed and the vibrations will be gone.
As it is, the TC distance to ground, or lack there of, is one of the Rubicons biggests downfalls. The other is the weak front axle shaft u-joint connections. I would discourage a TC lowering kit unless it is temporary solution.