The reason you have to swap the differential if you don't get a custom driveshaft is the differential casing of the 540i6 is a different size and shape from the iT. So even the 540i6 driveshaft will not be the proper length unless you have the 6 speed transmission and the 540i6's differential. A custom driveshaft would solve that problem.
Also there have been issues with cruise control when using a differential with gearing different from what the ECM expects. The good news is there should be quite a few 540i6 differentials available due to upgrades to M5 differentials.