To answer OP question, you don't have to completely remove the exhaust. In my experience, to gain access to the carrier pinion flange fasteners I just removed the exhaust flanges so that I can get the heat shield out of the way to get the carrier pinion fasteners out. Hopefully that helps..

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2003 BMW X5 3.0i -- MT5, 3.64s final gears, H&R lowering springs, K-Mac bushing kit
2007 BMW X3 3.0Si -- MT6