By reducing the amount of bump stop needed and raising the upper shock mount, you are able to better keep your suspension travel sprung and at full droop the axle is not pulled under the Jeep like it would be with the same length shock in the stock mount. The available sprung travel is detirmined by the coil springs solid height and free length. 2dr JKs are at a disadvantage compared to 4dr JKUs because the coils have a shorter spring length until you get into really tall lifts. When I first started looking at mild lift coils for my JK, alot of the 2"-2.5" lift coils had a free length comparable to some of the stock JKU coils.
With the exception of Metalcloak's 6 pack shocks, a shock with a long stroke has to have a fairly long collapsed length. To fit the long collapsed length shock without raising the upper mount or lowering the lower mount, you have to extend your bump stops. Bump stops limit/reduce suspension travel to prevent shocks from bottoming out and to increase tire clearance. If you rely solely on bump stops to give you the clearance needed for a shock with a long stroke, you end up trading sprung travel for un-sprung travel (after the coil spring reaches its free length and unseats from the coil bucket). Not a good trade in my opinion.
The 1.25" Body Lift made a big difference in increasing sprung suspension travel. It reduced the amount of bump stop needed for tire clearance by 1.25" (front and rear). The Body Lift also allowed the upper shock mount to be moved up an additional 1.25" which allows for a longer collapsed length shock that has a longer stroke. Even if you only credit the body lift for allowing for 2" of additional sprung travel, That's almost a 25% increase over stock and almost 15% of a 14" stroke shock. 2" does not account for the additional stroke in the longer collapsed length shock which also contributes to increased travel.
I wanted to limit the amount of bump stop needed for tire clearance to 2"-2.5" at most. The front has around a 2.25"-2.5" bump stop, the rear has 2" bump stops and I'm running a 38.5x13.50x17 Super Swamper Bogger (had to do a little trimming). The 37" Cooper STT Pros fit about as perfect as it gets though.
These show how the Ford mount was cut/notched to fit up against the coil bucket. It's a pretty easy cut to make and can be cut to adjust the angle and depth of the mount.