I have a friend who uses a JB in the bridge of all his LP Studios. He swears by the combination and I tried the guitar when demoing and amp I later bought from him. I totally agree, the JB really rocks. Pickups are all about what you are going for with a guitar / pickup / amp combination.
The Alnico II Pro / Custom Custom combination in my Godin LG was great for lower gain settings on the amp. When I wanted a dynamic tone with an absolutely gorgeous transition into clip, the darker and more powerful Seymour Duncans were perfect. The Rebel Yell, by comparision, is bright and sounds very thin in that same scenario. The trade off is how complex, crunchy, and articulate it sounds under higher gain settings. There's a reason people who like modern tones really dig BKP.
Additionally, for the same effect with the beautiful softer clip, the solution with the Rebel Yell is to turn down the volume pot. The results are surprisingly comparable.