If all you want is an N54 flash tune you can load it using the BimmerBoost software for free. MHD offers some additional features and data logging to flash mapping but you pay more for them and have to pay for their maps. The JB4 can be run with or without a backend flash map and offers many unique features not possible flash only (like startup-sweep, in dash boost gauge, in dash shift light, etc), unlike a flash only tune can be easily removed and resold later, and offers auto tuning. Eliminating the need for custom mapping and endless logging to setup your wastegates, fuel trims, mods, fuel mixture, seasonal weather changes, etc.
The thread with the JB4 back end flash maps explains some of the benefits of adding in a JB4 to the mix and why it's so wildly popular:
http://www.n54tech.com/forums/showthread.php?t=29236
Beyond that to let the thread continue will likely result in yet another tuner flame war so I'm just going to close it. You can ask follow up questions within the back end flash thread above provided the discussion remains civil.